Clarke, 34, was signed on a two-year deal last summer, but his contract has been terminated by mutual consent.
The form of Adam Smith meant Clarke made only four first-team appearances for the Cobblers last season and did not feature at all in the league.
Wimbledon, also promoted to League One via the play-offs, have not disclosed the length of Clarke's contract.
"It's a fantastic opportunity for me," he told Wimbledon's website.
"To join a club of this stature, with its history is an honour and a privilege. It's going to be an exciting season ahead in League One."
Clarke, who started his career at Bristol Rovers, joined Northampton after leaving Oxford United.
AFC Wimbledon have signed Ryan Clarke after the goalkeeper was released by Northampton Town.