The City striker was brought on in the 61st minute of the game in Porto Alegre with the game still goalless.
And within four minutes of Jesus coming on, Brazil had made the breakthrough, Everton striker Richarlison finding the target with a 65th minute effort with Ecuador goalkeeper Alexander Dominguez unable to stop his angled near-post shot.
Brazil then sealed the victory in injury time with a Neymar penalty after referee Alexis Herrera adjudged that Jesus had been impeded in the box.
The spot kick was awarded after a lengthy VAR review and though Neymar’s first effort was saved, the Paris Saint-Germain star was allowed to retake the kick after the referee spotted players encroaching into the penalty area.
The result means Brazil have won all five of their World Cup qualifiers.
They top the 10-team South America group with 15 points from five games, four ahead of second-placed Argentina. Ecuador lie in third with nine points having won three of their previous four qualifiers.
Brazil face another World Cup qualifier away to Paraguay in Asuncion on 8 June, while Ecuador host Peru the same day.