Billy Forbes excited the fans in the fifth minute as he skinned his defender and made a rampaging run in to the box, but was cut off when he tried to cut the ball to his preferred foot which allowed Atlanta to send it out for a corner, which they cleared.
Atlanta had a penalty appeal turned down as Jaime Chavez went down under pressure from Greg Janicki but the contact was minimal, if any, and that was matched by the half protests.
That was the start of a good period for Atlanta in the tenth minute and Kwadwo Poku nearly delivered a wonderful goal, but his strike from distance was right at the right level for Josh Saunders who made a solid save.
In the 13th minute a corner gave the Scorpions a phenomenal chance as Walter Restrepo's corner was flicked toward goal by Tomasz Zahorski but his effort was well cleared off the line by Lucas Paulini who hacked it away to safety.
Just over one minute later another Restrepo corner caused pandemonium in the box as a header for Billy Forbes went just beyond him but was nearly put in to the back of the net by Ryan Roushandel, who was spared by Eric Ati.
In the 20th minute the Scorpions attack were going for it again as a flowing move allowed BIlly Forbes to get space just inside the box, allowing him a powerful shot, which was well saved by Ati.
Cesar Elizondo had a golden opportunity on the half-hour as Restrepo continued his great match, sending in a ball across the deck which Forbes left for Elizondo, after the entire Silverbacks defense missed the ball, but Elizondo skied it.
The ball very nearly snuck in for the Scorpions in the 36th minute as Restrepo made a great run in to the box from the left and shot from a tight angle, which snuck under Ati's thigh but out for a corner.
After Atlanta half-cleared the corner San Antonio came working back in to the box, allowing Forbes to back-heel for Julius James to shoot, but it was cleared off the line by Blair Gavin.
San Antonio fans appealed for a penalty in the 44th minute as Elizondo was sandwhiched going up for a header, but the players on both teams and the referee seemed much less interested as play continued, ending the half scoreless.
The Scorpions started the second-half well as they controlled much of the early possession and in the opening minute Zahorski was able to cut in and make space but his shot from 20 yards went wide of goal.
Just four minutes in to the second half San Antonio opened the scoring as Zahorski replicated his earlier effort and Ati made a great save, only for Elizondo to run on to it and almost dribble it in to the back of an empty net.
A free-kick from Junior Burgos allowed Atlanta a golden opportunity and he found Poku who controlled but the Scorpions defense scrambled and cleared it for a corner which the Scorpions cleared.
After that scare the Scorpions really started to settle the match down and control proceedings as they looked to choke Atlanta out of the match.
In the 76th minute the Scorpions had a golden opportunity to double their lead as Ati came bounding out of his box but couldn't decide if he wanted to gather the ball and collided with Elizondo, allowing Restrepo to score from the spot, sneaking it under Ati.
In the 79th minute Atlanta pulled a goal back as a flowing counter attack allowed Junior Sandoval to hit the back of the net and give the Scorpions a nervy final ten minutes.
But the Scorpions managed to hold out despite a scare in stoppage time after an impressive free-kick but the flag gave the Scorpions the vital win.