With Brazil trailing 1-0 at half time in the early hours of Friday morning, Raphinha replaced Éverton Ribeiro before the start of the second half.
The Leeds star then set up the equaliser as he delivered the corner for Marquinhos to head home in the 71st minute.
He thought he had already helped Brazil to haul themselves level just before the hour when Thiago Silva headed the ball into net from Raphinha's free-kick before being flagged offside.
With five minutes of the contest remaining, Gabriel Barbosa gave the away side the lead from the penalty spot and Brazil made sure of their victory in the fifth minute of stoppage time.
Raphinha got to the byline and pulled the ball back for fellow substitute Antony to tap the ball into the net.
Venezuela had not beaten Brazil in a World Cup qualifier in 17 previous meetings but their hopes of ending that long run rose when Eric Ramirez scored for the hosts after 11 minutes.
Brazil were without star player Neymar due to suspension with it left to Raphinha to inspire his nation to victory in Caracas.
Argentina's 0-0 draw at Paraguay meant Brazil extended their lead at the top of the South American qualifying group to eight points.
In the South American qualifiers, the top four teams automatically earn a place in Qatar while the fifth-placed side goes into a play-off with a country from another region.
Brazil have two more fixtures before the international break ends and Leeds United fans can see how to keep up with them and Raphinha HERE.