Jorge Velasquez headed in another for Belgrano in the 16th minute, only to see his effort disallowed for offside, and the same player had another effort ruled out four minutes later, causing angry protests from the home team as television replays suggested he was onside.
Carrera then appeared to be tripped in the area, but play was waved on and Belgrano had another penalty claim for handball which the referee ruled to be accidental.
Boca took advantage by scoring an 86th minute winner with a Daniel Diaz header which deflected off a defender.
A blunder by goalkeeper Nicolas Cambiasso allowed Estudiantes beat All Boys 1-0 in another of Wednesday's matches.
All Boys keeper Cambiasso allowed a bounding 35-metre effort from Gaston Gil Romero to slip through his legs in the 31st minute, handing Estudiantes the points.
The game ended on an unhappy note for Estudiantes when 38-year-old former Argentina captain Juan Sebastian Veron, who came out of retirement last month, limped off and was seen placing an ice bag on his calf muscle.
(Reporting by Luis Ampuero; Writing by Brian Homewood; Editing by Amlan Chakraborty)
