Eduardo Sebrango struck his ninth and 10th goals of the season Sunday as the Whitecaps twice came from behind to gain revenge for their defeat in Atlanta five days earlier.
Ansu Toure put the visiting Silverbacks up 1-0, then ahead 2-1 with a brace of stunning first-half strikes, and the Georgia side looked set to send Vancouver spinning to their third successive USL First Division loss.
However, captain Jeff Clarke restored home morale with the first equalizer and then marshalled a rousing second-half comeback as the Whitecaps netted twice late on to remain joint-top of the league.
Clarke admitted the crucial win will be a huge confidence-booster.
"After the long road trip, to show the character and will to come back twice will give us a huge lift," he said. "We have almost reached the middle of August now, so those points will be worth double."
Sebrango's 88th-minute winner sparked furious protests from the Atlanta players, after substitute Geordie Lyall, making his first appearance of the season, floored visiting goalkeeper Felipe Quintero in attempting to meet Martin Nash's corner.
Clarke, though, said he felt it was a fair challenge and that, for the first time in a while, Vancouver had perhaps had the rub-of-the-green in terms of refereeing decisions.
The Whitecaps made an encouraging start, but couldn't make their possession tell - and it was the Silverbacks who made the breakthrough in the 20th minute.
Scott Buete fed Toure just outside the penalty area and the forward unleashed a swerving, dipping shot which smacked the underside of the crossbar and bounced down beyond the goal-line. The ball then spun out, falling kindly for the lurking Jerson Monteiro, who firmly headed it past Jay Nolly just to make sure. TV replays confirmed it was Toure's goal, however.
Within five minutes, Takashi Hirano made a crucial intercepting header to deny the Silverbacks a second goal-scoring chance, before the home side drew level.
Jason Jordans attempted pull-back was palmed into the path of Clarke by Quintero, and the home skipper made no mistake, drilling a shot into the bottom corner.
Parity was restored for only 14 minutes, though, as Toure bagged his and Atlanta's second goal in the 39th minute.
Buete was again the provider, slipping a ball to the forward who turned Wes Charles inside out and chipped a shot over the grounded Nolly.
The Whitecaps responded well to going behind again, Sebrango winning possession inside the Silverbacks penalty area and setting up Jordan. The latter, however, shot wildly wide.
Sebrango had golden opportunities to draw Vancouver level either side of half-time, curling a shot against the post just before it and then heading inches wide just after it.
Head coach Teitur Thordarson threw on substitutes Lyle Martin, Charles Gbeke and Geordie Lyall in a bid to spark a shift in momentum and it bore fruit 18 minutes from time.
Sebrango, breaking from midfield, put Gbeke in the clear, only for the striker to pull the trigger on a weak shot which was parried by Quintero. However, the ball squirted free and the Cuban forward reacted quickest to lash a shot into the roof of the net.
The long-time injured Lyall then played his part in creating the winning goal, going shoulder-to-shoulder with Quintero, before swinging in unison with Sebrango at the loose ball the latter claiming the all-important touch.
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