The City forward was substituted with 13 minutes to play, before Liverpool forward Roberto Firmino and Real Madrid’s Casemiro handed the Selecao a dramatic and controversial win.
Despite the late drama, it was Colombia who took the lead in spectacular fashion just after the ten minute mark when Luis Diaz found the back of the net with an emphatic overhead kick from Juan Cuadrado’s floating ball to the back post.
Unshaken, Brazil immediately sought a route back into the game, but were unable to carve out any truly clearcut chances in the face of a staunch visiting rearguard.
Firmino was introduced at half-time for Everton Ribeiro to aid the holders' cause, with Jesus operating in a wider role for the second 45.
Our number nine found some more joy out on the right and cut inside into a dangerous area early in the second period.
However, Jesus lost his balance at the crucial moment and couldn’t find the target with an effort on goal through a crowd of bodies from the edge of the area.
Nonetheless, the City man was enjoying a greater involvement in Brazil’s play, and turned provider soon after when he whipped a clever ball into the near post for the onrushing Firmino.
A timely interception from Spurs centre-half Davinson Sanchez, who was on hand to cut out the danger at the last moment, prevented what would surely have been an equaliser on the hour.
Jesus was brought off for Benfica’s Everton Soares as the game ticked over the 75-minute mark just moments before Firmino’s opener, which sparked lengthy protests from the Colombia players.
Neymar’s attempted ball through the visiting midfield deflected off referee Nestor Pitana and into the path of Lucas Paqueta, with the passage of play leading to Renan Lodi’s cross into the Liverpool man.
Firmino’s header squirmed under the body of David Ospina to hand the tournament hosts an equaliser and leave the Colombian players, who felt the incident had given Brazil an unfair advantage, incensed.
But there was further late heartbreak for Reinaldo Rueda’s side when an unmarked Casemiro powered home a header from Neymar's corner ten minutes into stoppage time to complete the turnaround, sparking huge celebrations from the Brazil players, substitutes and staff.
The victory means Jesus and co. are guaranteed top spot in Group B, with maximum points from their three matches so far.
However, they can still have a huge say on who else qualifies for the knockout stages when they face Ecuador in Goiania on Sunday 27 June.
Despite defeat, Colombia’s four points from four matches already sees them into the last eight while Peru, Ecuador and Venezuela battle it out for the final two spots this weekend.