Reyes connected for the second time in the series, helping the Mets take three of four from Cincinnati. The NL East leaders, who have won eight of 10 at home, remained 1½ games ahead of second-place Atlanta.
"We're going to get back to where we were last year when we ran away with it," Milledge said.
Adam Dunn knocked out a scoreboard panel with a long home run for Cincinnati, which has lost 14 of 20 on the road.
For the second day in a row, Milledge came through. The talented young outfielder, called up from Triple-A New Orleans on Thursday, doubled home two runs to cap a three-run second inning. On Saturday, he hit a tiebreaking single in the eighth inning of a 2-1 win.
Milledge also homered and drove in two runs Friday, and dashed around the bases to score the go-ahead run with a nifty slide in Thursday night's victory.
"I'm getting the job done here," Milledge said. "They're giving me a chance to play and I'm going to take advantage until Moises (Alou) comes back."
The Mets scored more than four runs for the fourth time in 12 games this month.
Activated before the game, Perez (8-6) allowed two runs and six hits in six innings. He struck out six, winning for the second time in seven starts. He had been sidelined because of a stiff back since his previous start June 26.
"Just what Dr. Altchek ordered," manager Willie Randolph said, referring to team physician Dr. David Altchek. "That's what (Perez) needs to do: focus and play strong."
Randolph said things are coming together for the rotation. On Monday, right-hander Jorge Sosa will come off the DL to start at San Diego.
"Anytime you have your rotation intact, that's what you're looking for," Randolph said. "Starting pitching sets the tone always."
Reds starter Kyle Lohse (5-11) threw 100 pitches but failed to get out of the fifth. He gave up five runs and six hits in 4 2/3 innings with three walks and three strikeouts. In Lohse's previous two starts, he had allowed two runs in 16 innings.
Interim manager Pete Mackanin said Lohse pitched well other than three mistakes, to Ramon Castro, Milledge and Reyes.
"His stuff was OK," Mackanin said. "He knows he made mistakes with those pitches and he paid for them."
It was the first time in eight games a Reds starter allowed more than three runs.
Reyes hit a two-run homer in the fifth, his sixth of the season, to give the Mets a 5-1 lead. He pumped his fist when the ball cleared the wall in right and rounded second base only steps behind Perez, who had singled ahead of him.
David Wright led off the three-run second for the Mets with a single past a diving Pedro Lopez at shortstop. Carlos Delgado walked on four pitches and Castro followed with a ground-rule double to center to score Wright. After Brandon Phillips extended fully to snare David Newhan's sharp line drive to second, Milledge doubled to right-center to score Delgado and Castro.
Dunn cracked the scoreboard in the fourth inning. His 460-foot homer hit high off the board in right field and appeared to dent the panel reserved for the Dodgers-Giants score -- a game that hadn't started yet. The panel was fixed before the top of the fifth. It was Dunn's 25th home run of the year.
"Well, gee, I hope they can find the money to pay for that somewhere," Dunn said, joking.
The Reds pulled to 5-2 in the sixth on three straight singles to start the inning by Norris Hopper, Jeff Conine and Phillips. Perez got Dunn to line out to center and then induced popouts by Edwin Encarnacion and Lopez.
"In the past, since I've been here, in the late innings we'd have really good at-bats. Now that is not what is happening," Dunn said. "I think it is a big problem. We have the worst record in baseball and that's not acceptable."
- The Mets activated Sosa from the 15-day DL and optioned RHP Mike Pelfrey to Triple-A New Orleans. Sosa will start Monday night at San Diego. Pelfrey was 0-7 with a 6.12 ERA in nine games, including eight starts.
- It was Military Appreciation Day at Shea Stadium, and four F-18s from the Marine Corps Air Station in Beaufort, S.C., performed a flyover after the national anthem.
- Phillips' second-inning single extended his hitting streak to 11 games. He is batting .375 (18-48) during that stretch.
- The Mets drew a franchise record 203,515 fans for the four-game series against the Reds. The previous record was 199,547 fans against Pittsburgh from July 29 to Aug. 1, 1988.