The game was rescheduled at Boca Juniors' Bombonera stadium from March 20 when it was abandoned after six minutes because of crowd violence at Velez's Fortin.
Velez went two points clear of River Plate to lead the Clausura standings with 21 points from 10 matches.
In a game played in two halves of 42 minutes each, striker Santiago Silva put Velez in front 12 minutes from time with a shot across the face of goal into the bottom corner from midfielder Victor Zapata's perfect crossfield pass.
The Uruguayan, joint top scorer in the Apertura championship with 11 goals, took his tally for the season to 16.
Midfielder Augusto Fernandez added the second in stoppage time, steering the ball home after fellow midfielder Ricky Alvarez had shrugged off two defenders on the right to feed him with a square ball.
The match from the sixth round of the Clausura a month ago was halted by the referee when visiting San Lorenzo fans broke down fencing behind one of the goals and their goalkeeper Pablo Migliore was hit by a missile thrown from the crowd.
San Lorenzo fans had clashed with police outside the stadium before kick-off after hearing a fellow supporter had died of a heart attack.
