Miami, which has suffered more losses (52) than any team in the National League, won for the seventh time in nine games.
Atlanta took a 2-0 lead through four innings, but Ruggiano came through with a two-out blast to left off Mike Minor (8-4) after Donovan Solano had opened the inning with a double and pitcher Ricky Nolasco had drawn a walk.
Adeiny Hechavarria added an RBI double in the sixth and a double by Jeff Mathis brought home two more Miami runs in the eighth.
The Braves had a four-game winning streak snapped.
Nolasco (5-8) went seven innings to get the win, striking out seven and giving up two runs on six hits.
After Mike Dunn gave up a run to the Braves in the ninth, Steve Cishek came on to record the final two outs and pick up his 16th save.