Adobe announced Lynch's departure in an 8-K filing along with its earnings report. Apple confirmed the move.
Adobe said the move is effective March 22 and that it will not be naming a new CTO.
"Responsibility for technology development lies with our business-unit heads under the leadership of Adobe CEO Shantanu Narayen," Adobe said in a statement.
Bryan Lamkin, who recently returned to Adobe, will assume responsibility for cross-company research and technology initiatives, and corporate development, Adobe said.
(Read More: Adobe Earnings Drop but Top Forecasts )
Lynch, known for his software chops, briefly overlapped with current Apple marketing chief Phil Schiller at Macromedia, where he started work in July 1996. In 1997, Schiller left Macromedia to join Apple in the early days of Steve Jobs's turnaround there.
At Apple, Lynch will report to Bob Mansfield, whose title is SVP of Technologies. Interestingly, Mansfield's responsibilities are listed as including Apple's wireless and semiconductor teams; software engineering falls under a different executive, Craig Federighi.
Mansfield and his team have broad influence over the direction of Apple's products, however. Mansfield has been actively involved in the development of Apple's cutting-edge hardware engineering efforts, including battery design, materials and wireless. And Apple's chips are custom engineered to boost the performance of Apple's operating system and applications.