Brainstorming a bit here... this is a potpourri of ideas, and I'm not sure I'd do all of them... I'd pick and choose based on nuances and gut instinct that are hard to put into writing...
Boss Relationship Stuff
It takes two to tango and @juliahayward is absolutely right that you probably can't fix the other guy (the boss). The best you can potentially do is get him framing the problem differently -- namely that when he makes you look bad, he looks bad, too, since he's the boss that should be responsible for helping you do things right. But that sort of profound learning is rare, and instigating it is hard.
Some ideas, on the boss-relationship front, just in case this isn't a complete and total loss:
Non-agressively get feedback -- very shortly after the next time he throws you under the bus after all the email checking you did - take him aside. Ask him why he did what he did. Don't frame it as an accusation... just something like "I'm trying to figure out your strategy here -- I'm trying to collaborate and I ran my emails by you. My impression was that you were OK with everything I proposed, but in that meeting just now, it sounded like you didn't support my actions... I don't understand".
- You can gently but firmly press the issue if he tries to evade. Avoid language that points to intent ("it looks like you threw me under the bus") - stick with the facts "you said you didn't agree with the email XYZ that I sent, but you approved it on Thursday"
- But you may also have to listen, say you'll consider it, and then go away and think about it. It's entirely possible that when you do, you realize it's all BS.
- He may try to put it back on you - which is probably BS.
If he's a schemer but not a jerk, he may confess that he's trying to set up a sort of bad-cop, good-cop situation and you are unfortunately the bad cop. That could be legit, but if he can't show you a way that he IS getting your back, despite the stuff he's letting you take the blame for - then don't trust him.
Investigate patterns - does he only do this to you? Who else does he do it to? Is he biased for/against any groups of folks? Or is it just you? Or everyone?
- Corollary: What happens to the other bus-throwing victims?
Either way - keep up that paper trail. A paper trail you don't need to use is a good thing. A paper trail you need but don't have is a terrible thing.
Get Your Own Back
Once you're at the "don't trust this boss" place, take this somewhere else. HR, a boss one level up, or another ally/advocate in a management role in the company are all decent choices, depending on who you trust the most and/or how your company runs.
Human Resources can be great in some cases, and terrible in others - even w/in a single company. If lots of folks are complaining about this guy, you've got a likelihood of safety in numbers. The tough role of HR can be that they are there to keep the company safe from lawsuits more than they are on the side of always being fair to every employee... so you have to work with that slightly off alignment. Thus a advocate or mentor can be helpful here, since you can get the gist of how to frame this in a way that clarifies why HR should get YOUR back.
There's also the 'get a new job' front -- for me a #1 indicator that I need a new job is when I don't trust my boss. If I can't trust the person most directly responsible for my current job success/failure - it's time to run.
Rock the Organization
This is the equivalent of making your self a bus-throwing-prevention shield. This is stuff your boss should be teaching you or getting you help with... but it seems he sucks at this.
This is coming from the Contentious Inter-Org Handbook...
Build a network in every org you have to work with. That's people you can talk to w/out formal communication, who you trust, who trust you. Use them to get a read on how best work between your orgs. They can give you insight, tell you the common point of view where they are, and maybe help brainstorm ways to not have the fight that creates the bus in the first place. FYI - the higher you rise in an organization, the less likely it is that your boss will help you do this...
Look at reasons for inter-org contention - the network helps, but there are also reasons that may be right out in the open. For example - it's not unlikely that any group with auditing responsibility will make any part of the organization that gets audited somewhat defensive. Ask questions, rephrase other people's point of view to make sure you have it, asking "what would help?", instead of "when can I have this?" may be the key to becoming their new favorite person. At some point, it's in the company's best interest for both sides to succeed, or they wouldn't pay both departments... look for that best interest and build from there.
- Use all forms of communication effectively:
- Email is great for longer messages, and a time delay
- IM is great for short fast messages
- all written forms are short on emotional context, so it's easy for people to get more steamed up in writing where tone of voice is often lost.
- calling (or video chat) is a great way to build better communication - as long as the other side will pick up the phone. It does, however, require both sides to be available at the same time.
- in person is often the most excellent way and if you don't do it alot, making the extra effort may be deeply appreciated. But distance can be a barrier in a disbursed company.
- eating together is strangely magical - many fights get fixed over lunch or even coffee.
- there are some generational differences -- folks who are not texting all the time may find it more alienating and I hear (can't say with experience) that millennials may find real-time conversation (phone, in person) - too intimate. Similarly, introverts may appreciate the pacing of text communication in a way that extroverts find annoyingly slow.
When you're on shaky ground (boss not supporting you!) - then the non-recorded forms of communication can feel terribly risky. A way to buffer that risk is to write summaries after any realtime/hard to record chat - it's actually a great way to keep everyone accountable - mailing a quick "thanks for the talk today! it really helped! here's what I think we discussed and here's what I think the next steps are... does anyone have corrections?" to everyone involved is actually a great way to capture the output of a tricky meeting. NOTE: This is for the more public stakeholder type conversations. If you do that sort of thing in your personal network, it may be seen as excessively formal.
When you have disagreement brewing, break the formality/remoteness of text based communication and go in for a quick phone call or in person chat... it's harder to be a jerk in person (for everyone!), so eliminate the jerk factor.
I would hope that in a good boss/employee relationship, you'd read this section and think "duh, @bethlakshmi, I know that..." because your boss would have taught you. And instead of throwing you under the bus, if you missed out on this stuff, he'd be covering you in public and giving you feedback in private. And if there was a way you couldn't possibly win the inter-org communication challenge - then he'd tell you, so you could prepare for that and react calmly.
But I strongly suspect your boss is not this savvy. That he's in over his head and doesn't know what do when other organizations give you both problems, so he throws you under the bus in an act of self-defensiveness... rather than himself doing the stuff I outlined here and then leading by example. So I say - if you like the company enough to stay -- work on this stuff, and get mentors from outside your broken business unit/area - so you can get good at this stuff.