Something like:

Dear CEO,

Thanks for your kind words and extending your support towards obtaining your degree. Everything I have learnt in last 2 years, have been extremely helpful in achieving this milestone and I owe it to you and all my colleagues and mentors here. Looking forward to continue my learning journey at XXX company.

Regards,

Happy Pumpkin

Something like:

Dear CEO,

Thanks for your kind words and extending your support towards obtaining my degree. Everything I have learnt in last 2 years, have been extremely helpful in achieving this milestone and I owe it to you and all my colleagues and mentors here. Looking forward to continue my learning journey at XXX company.

Regards,

Happy Pumpkin