The Tractors continued to push forward, and nearly broke the deadlock when Massimo Luongo saw his effort fly just past the post on the half-hour mark.
Jay Emmanuel-Thomas had the first chance of the second period, flashing an effort just wide five minutes after the restart. Chopra was then guilty of missing the best chance of the game as he touched Martin's cross wide.
Luongo was given another chance to break the deadlock after some fluid passing by the visitors, but his shot went narrowly wide.
The deadlock was finally broken in the 90th minute as Chopra slid in to give the Tractors all three points with one of the last kicks of the game.
Ipswich face Blackpool on Saturday, while Watford will host Birmingham City.