The right-hander popped a fourth-inning, three-run homer that eventually proved to be the difference in the Stars' 5-4 win over Mississippi.
With two outs and two men on in the top of the fourth, Thornburg (2-0) sent a Zeke Spruill fastball over the left-field wall for his first professional home run.
"I was pretty happy about it, thought I hit it pretty well," said Thornburg. "It was funny walking into the dugout, everyone was just smiling. It felt good. Every time a pitcher hits a bomb, it's so unexpected, so people are like, 'What the heck?' or 'Wow.'"
Milwaukee's No. 4 prospect retired two of the first three batters in the sixth, and then the Braves' Adam Milligan reached on first baseman Hunter Morris' fielding error and Christian Bethancourt eked out an infield single.
Cory Harrilchak's bases-loaded double off reliever Darren Byrd plated all three runs. But it was all the scoring the Braves would muster and Thornburg's second win was preserved.
"In the sixth it was really humid, you're sweating a lot so it's kind of hard to grip the ball," said the 2010 third-rounder. "I walked a guy, there was an infield hit and an error. Not too much you can do about it, can't really complain.
"It was definitely one of those good nights overall. You know I ended up needing that home run, otherwise I would've gotten the loss. But it feels great to get out there and get the win."
Thornburg wound up allowing four runs -- one earned -- on four hits and three walks while striking out seven over 5 2/3 innings. The effort dropped his ERA back below two at 1.93 and his seven strikeouts give him 33 over 28 innings against seven walks through his first five starts.
The Houston native said he worked mostly with his fastball, and partially fell into trouble because he wasn't locating his off-speed pitches with consistency.
"I'm definitely happy to have the second win," he said. "I was hoping to get to it a bit earlier, but 2-0, I'll take it."
Right fielder Kentrail Davis, the Brewers' No. 9 prospect, provided Thornburg with his first two runs when he drove a two-run double to left in the third.
Robert Wooten closed the door on Mississippi, striking out two in a perfect ninth for his fourth save.