Ty Wigginton homered and the Astros beat New York 4-0 to finish their first three-game sweep of the Mets since September 1993.
The Astros are still four games under .500 and a long way from contending in the NL Central. But they've won five of their last six series and can make up ground when they open a three-game series against first-place Chicago on Monday.
"It feels good at this time," said Wigginton. "We've just got to come out and continue playing good baseball."
Jose Valverde shut out the Mets in the ninth. Houston's bullpen did not allow a run in 11 innings in the series.
New York has dropped four in a row and was shut out for the fourth time this season. And the dismal offensive performance was only part of the bad news.
Closer Billy Wagner was unavailable with a strained left forearm and was due to have an MRI exam in New York on Tuesday. The Mets also placed right-hander John Maine on the disabled list to further rest his sore right shoulder.
The Mets open a seven-game homestand on Tuesday after dropping five of six games on this road trip.
"We just need to get home, get ourselves together," said Mets manager Jerry Manuel.
Oliver Perez (7-7) took Maine's place in the rotation on Sunday and lost for only the second time in seven starts.
Wigginton gave the Astros a 1-0 lead with a solo homer in the second, his 10th. The Astros have homered in eight consecutive games, a season high.
The Mets loaded the bases with one out in the fourth and fifth and came away with nothing. They also squandered a no-outs, bases-loaded chance in Friday's 7-3 loss.
New York went 1-for-10 on Sunday and 6-for-26 in the series with runners in scoring position.
"We definitely had some opportunities. We really didn't take advantage of them," Manuel said. "But I feel real confident that we'll turn this around and swing the bats the way we're capable of."
The Astros stranded only four runners in the game and scored three runs in the fourth, all with two outs.
Back-to-back doubles by Wigginton and Pence made it 2-0 and Pence scored on Darin Erstad's bloop single to left. Quintero then doubled down the left-field line and Erstad raced home for a 4-0 lead.
After hitting .304 in July, the Mets mustered only seven runs in three games in Houston.
David Wright, who went 3-for-22 on the road trip, said the Mets' slump is temporary, part of the usual ups and downs of a season. But he said the Mets can't wait much longer to break out of it.
"Now's the time we've got to bear down," he said. "We don't want to be scoreboard-watching later on. We don't want to wait 'til September to make our move. We have to push ourselves and get it going again."
The Mets stranded 11 runners on Sunday and a total of 24 in the series.
"I'm hoping it's a bump, not a hill," Manuel said. "We should be OK. Some of the guys, I won't say they were pressing. But in situations, we weren't getting hits."
Chris Sampson relieved Wolf for the sixth and set down the Mets in order, all on ground balls. Wolf, acquired in a July 22 trade with San Diego, threw 96 pitches, allowing six hits with seven strikeouts.
Eddie Kunz, whose contract was puchased before the game, made his major league debut in the seventh, taking over for Perez.
Erstad led off by beating out a bunt. Quintero laid down a sacrifice bunt and Kunz fielded it, but his throw to first sailed over Carlos Delgado's head, the Mets' first error in 12 games. Delgado recovered in time to throw out Erstad at third.
The Mets had runners on first and second with no outs in the eighth, but Damion Easley rolled into a double play against Doug Brocail. Nick Evans grounded out to end the inning, another missed opportunity.
"We haven't been very good in situational hitting," Manuel said. "We've got to find a way to get better at that."
"Their bullpen came in and it seemed like this whole series, they shut us down," Wright said.
Kaz Matsui and Fernando Tatis both extended their hitting streaks to 10 games. ... The Astros won a series from the Mets for the first time since July 2005. ... Mets manager Jerry Manuel tentatively planned to start Maine again on Aug. 13 at Washington. ... Astros CF Michael Bourn was out of the lineup for the seventh straight game with a sprained right ankle.