The Mets announced the deal before Saturday's game against Atlanta. The sides reached agreement earlier this week, pending a physical.
The 25-year-old Niese went 11-11 with a 4.40 ERA last year. He'll make his first start of the season Sunday against Atlanta.
This was the Mets' first big move since settling the lawsuit by the trustee in the Bernard Madoff Ponzi scheme and securing $240 million from a dozen minority investors.
Mets general manager Sandy Alderson says Niese's deal might've gotten done anyway, but added it was "hard to ignore" that those financial issues had been resolved.