A maiden goal for 19-year-old Daisy Brown in the 56th-minute gave Brisbane the ascendancy in Sunday's match at the Home of the Matildas.
But Victory pushed hard for an equaliser at the death and looked set to get it when Rhianna Pollicina's through ball set up Kennedy White for an excellent chance.
The Roar hadn't kept a clean sheet all season, and Lincoln simply refused to let that rut continue, going low to block White's strike with her legs.
It helped secure Brisbane's second win over Victory this season, marking the first time they had beaten the powerhouse team home and away since the 2012/13 campaign.
"My heart stopped in that moment, but it shouldn't have, because Chloe is so reliable back there," Roar defender Marianna Seidl told Paramount.
"She makes some unbelievable saves and she definitely kept us in this match."
The win lifted Brisbane (13 points) into sixth spot, while fourth-placed Victory (16 points) missed the chance to go equal top.
"I just think we're missing goals at the moment," Victory captain Kayla Morrison told Paramount.
"We defended pretty well. Their goal was an unlucky goal - maybe the wind had something to do with that. We're keeping the ball well, but we're not punishing teams.
"We're trying to find what the answer is, because we look around the group, and we look at the players we have, and the way we're performing is just absolutely unacceptable."
With Matildas coach Joe Montemurro an interested onlooker, Brisbane's defence absorbed plenty of pressure in the first half while also creating some good chances.
Roar midfielder Sharn Freier had her early shot blocked, while Bente Jansen created herself a great chance in the 19th minute, only for her strike to go straight at the goalkeeper.
Victory players were left frustrated when their calls for a handball in the box were waved away in the 10th minute.
Roar defender Leia Varley seemed to pivot her left elbow into the path of Pollicina's thunderbolt strike - with the movement blocking the shot.
Brisbane started the second half with a bang.
Brown had two quick chances to open the scoring - her mid-range shot was blocked, and a short time later her attempt at the near post was also stifled.
But it was a case of third time lucky when Brown was able to bundle in Marianna Seidl's corner from close range, with Lincoln's late goalkeeping heroics ensuring Brisbane walked away with all three points.
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