The GreenJackets (21-26) gave up seven runs on 15 hits after allowing just three runs combined in the first two games of the series.
The Augusta bats, which entered the game with a South Atlantic League-worst .212 team batting average, got four runs on eight hits, including a two-run second aided by a Savannah error and wild pitch.
The Sand Gnats (29-19) countered with a three-run third off GreenJackets starter Kevin Couture (2-3). The 32nd-round draft pick suffered his worst outing as a starter, giving up four runs on nine hits and two walks over four innings.
The GreenJackets bullpen, which had thrown 11 consecutive shutout innings entering the night, got two more from Aldaberto Mejia and another one from Steven Neff before Neff allowed an eighth-inning run on a Charley Thurber double and Gilbert Gomez two-out single.
Keith Bilodeau gave up two more Savannah runs on extra-base hits from Dustin Lawley and Travis Taijeron in the ninth.
Sand Gnats starter Rafael Montero (4-2) got the win after allowing three runs over seven innings. He walked none and struck out four.
T.J. Chism threw a perfect ninth to get the save.
The two teams will wrap up the series with an afternoon game Sunday.