The five-time world champions had taken a sixth-minute lead in Brasilia through a Raphinha penalty only for Luis Diaz’s fine 41st-minute strike for Colombia to level the game on Thursday.
Colombia enjoyed the most pressure in the second half but were ultimately sunk by the Real Madrid winger’s dramatic winner.
The victory leaves Brazil well positioned in second place in the 10-team CONMEBOL qualifying group, four points behind leaders Argentina who travel to Uruguay on Friday.
A foul from Daniel Munoz on Vinicius resulted in the early penalty for Brazil and Raphinha, taking a short run-up, confidently slotted home the spot-kick to give the home side an early lead.
But four minutes before the break, James Rodriguez found Liverpool’s Diaz on the left and the winger moved inside before driving it home into the far, bottom corner of the net.
Rodriguez had an opening in the 68th minute, after a smart move from Colombia, but the playmaker’s shot was comfortably dealt with by Alisson Becker.
Diaz’s Liverpool team-mate Becker had to go off injured in the 78th minute, with an apparent concussion, after a collision with Colombia’s Davinson Sanchez which resulted in the defender being stretchered off.
While Colombia enjoyed the bulk of attacking possession, Brazil remained a threat and Guilherme Arana flashed a shot wide in the 82nd minute.
The Alisson injury had created the lengthy stoppage time and Vinicius took advantage with his fiercely struck effort taking a slight deflection off a defender’s head and flying in.
“Today’s goal is a bit of relief, a bit of happiness. Playing for the national team is something you can’t explain,” said Vinicius.
“Every time we come here, it’s like it’s the first time”.
Brazil face old rivals Argentina on Tuesday.
It was a bitter ending for a Colombia side who sit in sixth place still with work to do in qualifying.
“We kept Brazil in their half, I think we deserved more again, but that’s the way it is. I have a lot of doubts about the refereeing decisions, which I’m not going to comment on,” said Colombia coach Nestor Lorenzo.
“We played a great game and came away with nothing again. We conceded a very early goal again,” he lamented.
In other South American qualifiers on Thursday, Paraguay beat bottom-placed Chile 1-0 in Asuncion, a result that left La Roja rooted to the bottom of the table.
Veteran 41-year-old striker Paolo Guerrero was on target as Peru beat Bolivia 3-1 to move off the bottom.
Andy Polo opened the scoring in the 37th minute before Guerrero found the target on the stroke of half-time. (AFP)
Bolivia pulled one back with a Miguel Terceros penalty in the 58th minute before Edison Flores restored the two-goal cushion in the 82nd minute.
