The GreenJackets (24-33) managed just four hits over eight scoreless innings until a walk and infield single in the ninth set the table for pinch hitter Ben Thomas, who launched a game-winning double to the center field wall.
The left-handed Thomas, originally slated for a day off, pinch-hit for the right-handed Jose Cuevas with a right-hander on the mound. Thomas hit a 2-1 fastball over the head of center fielder Brent Keys to score Shawn Payne and Jose Flores.
The improbable victory came one night after the GreenJackets won the series opener by scoring the game’s only run without the benefit of a hit.
The two wins came against the Miami Marlins’ top two draft picks from 2011.
Second-rounder Adam Conley took a no-hitter into the sixth Tuesday before suffering the loss, and first-rounder Jose Fernandez, named the Northern Division’s all-star starter earlier this week, got a no decision despite throwing seven scoreless innings.
“That was another pitcher, God bless him, who will have a bright, bright future,” Augusta manager Lipso Nava said.
“It feels good for us as a team to come together, snap that losing streak and do it against what’s probably the best pitching in the league.”
Fernandez (6-1) used a 98-mph fastball and breaking pitches in the low 80s to limit the GreenJackets to three hits and a walk over seven scoreless innings.
Starter Chris Marlowe, last year’s fifth-round pick by the Giants, kept Augusta in the game, allowing just one run on three hits over five innings. He walked four but struck out five in a no decision.
Greensboro (40-19) scored its lone run in the fourth after Keys led off with a walk and took second on Marlowe’s wild pitch. Ryan Rieger drove the run in on a groundball double down the right field line that snuck inside the bag and just out of reach of first baseman Wes Hodges.
Greg Nappo (0-3) relieved Fernandez and threw a scoreless eighth but gave up an infield single and walk in the ninth. Brad Mincey took over and surrendered the walk-off double.
Nava used his relievers freely.
Paul Davis, Steven Neff and Derek Law (3-0) combined to throw four scoreless innings and give the GreenJackets a chance.