The Mustangs lost 5-4 in walk-off fashion in Game 1, then fell 9-5 in the nightcap.
Milton (25-7) moved on to the semifinals to face either Valdosta or north Fulton rival Johns Creek.
Kennesaw Mountain (24-8) came from behind in both games, only to fall short.
The Mustangs came back from 3-0 and 4-3 deficits in Game 1 before Jack Thompson’s one-out single sealed the win for Milton.
Game 2 saw Kennesaw Mountain battle back from deficits of 3-0 and 4-3 to take a 5-4 lead heading into the final inning, but Milton scored five runs off six hits in the top of the seventh, and the Mustangs went down quietly in the bottom half to end their season.
Milton produced 26 hits in the doubleheader — including 17 in Game 2 — compared to only nine overall for Kennesaw Mountain.
“Give (Milton) credit,” Kennesaw Mountain coach George Hansen said. “They hit the ball well all night and put it in play. We hit well, too, but a lot of them to their players.
“Our (pitches) didn’t move as well as they should have. Milton also bunted well and had big hits and, on a lot counts, they were behind, and they finished plays.”
Milton pitcher Matt Geiger had a no-hitter through five innings of Game 1, and the Eagles’ offense took advantage of the Mustangs’ miscues to build their 3-0 margin.
After Ryan Gridley was hit by a pitch to lead off the game, back-to-back errors put him at third. Dylan Cease’s RBI single then brought him home for a 1-0 lead.
Erik Petersen walked to lead off the third and later scored off a throwing error as Dalton Ewing stole second.
Milton built its 3-0 lead when Ewing’s RBI double that plated Petersen in the fifth.
Kennesaw Mountain didn’t go down without a fight, however.
Reggie Pruitt produced the Mustangs’ first hit with a leadoff single in the top of the sixth. Michael Atkinson then walked before Tyler Stephenson blasted a home run on a 2-2 count to knot the contest at 3-all.
Milton recovered with a run in the bottom of the sixth. Clayton Vaught hit a one-out single and got to second on a fielding error. He later scored on a two-out error that put the Eagles ahead 4-3.
The Mustangs rallied again when Zack Goodman’s two-out homer knotted the contest at 4-all.
Kennesaw Mountain’s rally ended in the bottom of the inning.
Milton pinch-hitter Chris Purpura led off the frame with a single, moved to second on Ewing’s sacrifice bunt and scored the game-winner on Thompson’s single.
Kennesaw Mountain starter Ryley Gilliam allowed four runs — though only one was earned — off six hits and struck out five in 5 1/3 innings.
Milton took a 3-0 lead through the first two innings of the nightcap, behind Cease’s RBI groundout in the first and Steven Curry’s two-run home run in the second.
Kennesaw Mountain tied the contest in the bottom of the third. Pruitt led off with a single and scored on Stevenson’s RBI single. Two batters later, Garrett Blinkhorn’s two-run double plated Atkinson and courtesy runner Hampton Clark.
Milton grabbed a one-run lead in the fourth when Gridley singled, moved to second on a balk, reached third on a sacrifice bunt and scored on an error.
The Mustangs grabbed their only lead of the series in the fifth. Back-to-back walks to Atkinson and Stephenson led off the inning, and a throwing error allowed Atkinson and Clark to score again, putting Kennesaw Mountain in front 5-4.
Down to its final three outs, Milton rallied in the seventh.
Vaught’s two-run triple plated Thompson and Farkas, while Dalon Farkas, Curry and Gridley each had RBI singles.
Milton reliever Will Matthews retired the side in the seventh to close out Milton’s victory.
As Milton looks to win its second straight state title, Kennesaw Mountain will have to be satisfied with winning the Region 4AAAAAA championship.
“Our season wasn’t a disappointment,” Hansen said. “We won the region, and we won 24 games and made the quarterfinals. We have a ton of guys coming back, and I think this team is ready to handle the pressure next year. They just have to live up to it. We had a great run.”