Cueto lasted just 4 1/3 innings after allowing a season-high six earned runs on nine hits.
"I don't know how to say what happened," said Cueto, who lost three starts in a row for only the second time in his career. "You have to take it easy. Things happen and thank God I feel healthy. I feel good. I just got to keep going."
During the month of September, the Reds are 6-7 with 36 runs scored. They currently sit 11 games in front of the Cardinals in the National League Central, and their magic number to clinch the division improved to six with the Cardinals' 4-3 loss to the Dodgers.
For the second night in a row, Miami took an early lead, this time with three runs in the first.
Consecutive one-out singles by Justin Ruggiano and Jose Reyes set up Giancarlo Stanton's triple. Stanton raced home on Carlos Lee's sacrifice fly to right, just getting under Ryan Hanigan's tag.
"His velocity is better than it's ever been," Reds manager Dusty Baker said of Cueto. "He was 95-96 [mph]. He lost location. He was either wild high or missing away. He came in there with strikes down the heart of the plate and those are the ones that hurt him. That's the main thing is location, location, location, and we've got to find Johnny's release point to get his location back."
Cincinnati chipped away at the 3-0 deficit with a run in both the third and fourth innings off Mark Buehrle.
Hanigan singled to open up the third and moved to second on Cueto's sacrifice bunt. After Brandon Phillips struck out swinging, Wilson Valdez blooped a ball into left to score Hanigan.
Valdez, who has started seven of the past nine games at shortstop with Zack Cozart out with a left oblique strain, is 5-for-15 over his past four appearances.
Jay Bruce snapped his 0-for-18 skid with a one-out triple that Stanton couldn't come up with in the right-center gap. Scott Rolen drove him in with a swinging bunt in the fourth.
But Miami tacked on three more in the fifth, punctuated by Lee's two-run blast to left that sent Baker to the mound to lift Cueto.
Reyes' RBI double to right drove in Ruggiano, who started the frame with a double to straightaway center. Lee connected on a 3-1 pitch for his ninth dinger of the season.
Six of the nine hits allowed by Cueto went for extra bases.
"In that situation, I was ahead in the count, and he threw the ball right down the middle," Lee said. "I would say he couldn't spot his breaking ball for a strike consistently. And we weren't swinging. That's the key right there. We were patient enough to stay off his pitches. I think that was the key, he couldn't spot his breaking ball, and we were patient."
Ryan Ludwick's 26th long ball of the year -- a two-run shot to left -- made it 6-4 and forced Buehrle out of the game. It marked his first homer since Aug. 18.
Asked whether Cueto -- already at a career high in innings pitched (197) -- would get pushed back, Baker said he didn't know yet. "We haven't had time to talk about it."
"We're not swinging the bats as good as we like," said Hanigan, who went 1-for-3. "Trying to get hot offensively and get them tomorrow. The offense has been a little slack. For whatever reason, we're getting our hits, but we're not coming up with the big hits when we need them. We've got to keep at it and hope we can change that."