TV replays showed San Lorenzo should've had a penalty when Fernando Tobio clearly tugged at Santiago Gentiletti's shirt three minutes before half time.
Velez pushed forward in the last 30 minutes of the game and almost scored when Allione's curled shot from the edge of the area struck the left post, with Torrico beaten.
San Lorenzo - one of Argentina's "big five" teams - won its 12th title of the professional era, with the start of the game suspended for 30 minutes due to legal problems in opening the stadium, which were resolved 90 minutes before the game was due to start.
Newell's opened the scoring in the 53th minute through Pablo Perez, before Paolo Goltz headed in to level the scores two minutes later.
Lanus' Carlos Izquierdoz conceded an own goal to put Newell's back into the lead, but Jorge Pereyra equalized for Copa Sudamericana holders Lanus in the 74th.