Velez advanced to the third round of South America's second-tier continental competition after Belgrano midfielder Esteban Gonzalez dragged Agustin Allione down in the box and Lucas Pratto converted from the spot.
Pratto's penalty secured a 2-0 win for Velez in front of their home fans, which was enough to overcome their Primera Division rivals on aggregate.
Velez levelled the tie in the 29th minute of Thursday's second leg after a brilliant move involving five players.
Left-back Emiliano Papa started the move with a pass inside to Alejandro Cabral, who linked with Allione on the left flank.
As Papa overlapped, Allione slid the ball back to Cabral on the edge of the box and the 25-year-old midfielder back-heeled to Hector Canteros.
Canteros pierced Belgrano's defence with a through-ball to Allione and the teenage winger squared a pass for the onrushing Ezequiel Rescaldani to score.
In a tense second half and with the tie in the balance, Velez eventually notched the crucial second goal after Allione got past Gonzalez only for the Belgrano midfielder to tug on the 18-year-old's arm and concede a penalty.
Pratto stepped up to the spot and side-footed his shot into the bottom corner to clinch victory for Velez.
In Sangolqui, Ecuador, Universidad de Chile scored twice in the final 20 minutes to secure a 4-2 aggregate win over Independiente del Valle.
Universidad were held to a 1-1 draw at home but took the lead on the night and on aggregate when Isaac Diaz scored in the 27th minute.
Independiente equalised three minutes later through Armando Solis but Universidad triumphed thanks to Charles Aranguiz and Luciano Civelli's strikes in the 70th and 86th minutes respectively.
In other results, Colombia's La Equidad advanced on away goals after a 1-1 draw at Cobreloa of Chile and Ecuadorian club LDU Loja triumphed 1-0 away to Paraguay's Nacional Asuncion.
