Controversial Estonia winner sinks Northern Ireland
Vassiljev's superb 30-metre strike six minutes from time came when Northern Ireland stopped playing after seeing the assistant referee raise his flag for offside against Estonia's Martin Vunk.
But referee Manuel Grafe waved play on and Vassiljev lashed home from outside the box.
The same player, who entered Windsor Park game on 65 minutes, had hauled Estonia level from the penalty spot after he had been fouled by Craig Cathcart.
Northern Ireland captain Steven Davis marked his 50th international appearance by firing the home side ahead midway through the first half after Estonia keeper Sergei Pareiko had fumbled Kyle Lafferty's cross.
Estonia, on 16 points, moved ahead of Serbia into second place in the group but have completed their campaign. Serbia will deny them a play-off berth if they win their final match away to Slovenia on Tuesday. Northern Ireland stay on nine points.