The Pro12 champions struck in the dying seconds, claiming a 20-18 pool victory.
The assistant referee, who had taken over as referee following an injury to Jerome Garces, awarded a penalty to Connacht after time had elapsed.
European Professional Club Rugby have said that the result will stand.
In a statement, EPCR said: "EPCR would like to clarify an issue arising from yesterday's European Rugby Champions Cup, Round 4 match between Connacht Rugby and Wasps at The Sportsground.
"The assistant referee, who had taken over as match referee following an injury to Jerome Garces, awarded a penalty to Connacht after time had elapsed.
"Connacht kicked the ball into touch, and from the resultant line-out, scored a converted try to win the game 20-18.
"However, as time had elapsed, Connacht should not have been permitted to take a line-out throw-in once the ball had been kicked into touch, as stipulated in Law 5.7 (e) of World Rugby's Laws of the Game.
"EPCR would like to thank all parties for their understanding, and would also like to confirm that the result of the Pool Two match stands."
Going into next month's final two rounds of group fixtures Wasps, Toulouse and Connacht are level on 13 points.
Tournament organisers have said that Connacht should not have been awarded the late line-out from which they scored their winning try against Wasps in the Champions Cup game on Saturday.