"He had enough rest," said Manuel after the win.
Thanks in part to John Buck's long run for a two-out, nobody on, foul pop by pinch-hitter Laynce Nix that clanked off Buck's glove in front of the Philadelphia dugout, the seventh turned into a long inning for the Mets.
When the reprieved Nix and Jimmy Rollins followed with hits and Mets manager Terry Collins went to reliever Scott Atchison, Howard doubled on a 2-0 pitch to the last foot of the warning track in center field to score both runners, breaking a 1-1 tie.
Chase Utley chased in Howard with a single to left-center field, John Mayberry Jr. scored Domonic Brown with an eighth-inning double and Antonio Bastardo, Mike Adams and Jonathan Papelbon each pitched a scoreless inning, making Cole Hamels a winner for the first time this season.
Hamels, lifted for Nix after six walks had inflated his pitch count to 111, allowed just two hits over six innings, despite his command issues.
"It wasn't any particular pitch," said Hamels. "I was able to throw them all for both strikes and for balls.
"I wasn't able to get ahead of hitters, so I just tried to plug away, not let the game get out of hand. You would rather give up hits than walk everybody and much rather go deeper into the ballgame. But sometimes you have to shake your head and move on."
The Mets hit only one ball hard -- Ruben Tejada's leadoff double -- regardless. The Phillies, who left the bases loaded in the first, when Brown topped a ball inches in front of the plate, were also struggling against Jon Niese until Freddy Galvis tied the game with a leadoff fifth-inning homer.
"Freddy has gotten bigger and stronger, he can hit the ball out of the yard when he catches it right," said Manuel.
Niese, unshaken, retired eight of the next nine Phillies until the dropped foul popup changed everything.
"I was watching it the whole way, and that was a tough play," said Nix. "It was four or five rows deep and then came back."
Nix drove his second chance into the hole between second and third, and Rollins singled on the ninth pitch of an excellent at-bat. Niese, believed Mets manager Terry Collins, was ready for a rest. But Howard's was over.
"I knew they were going to put Howard in, but I don't care who it is, Atchison's ball is really difficult to hit," said Collins. "The issue is he fell behind and tried to sneak a fastball in."
Six innings had not put any rust on Howard's swing.
"It's not really an off-day," he said. "It's just a day you don't start.
"Even though you don't start a game, you still remain in it. You watch the flow of the game, because you know there is going to be a situation when you can come up and pinch-hit. Usually it's a situation where you can turn the tide of the game."
With Howard's key knock, the Phillies celebrated Carlos Ruiz's return from a 25-game suspension with a ninth win in their last 10 games against the Mets. Ruiz, who had only 14 Minor League at-bats to get ready, doubled and hit two other balls hard. Manuel said he wasn't surprised.
"I expected him to go 4-for-4," the manager said, tongue only partly in cheek. "I expect all our guys to do well every day.
"Chooch has become a good hitter over the last two years. He is a big player in our lineup. With Delmon Young [rehabbing a surgically repaired ankle in the Minors], that can give us a different look. We can throw more right-handed hitters at left-handed pitchers.
It was the first series sweep of the season for the Phillies, all of whom get Monday off before opening a two-game series Tuesday in Cleveland. One day later, their manager doesn't think rest is such a hot idea.
"I want to keep playing," said Manuel. "We're starting to play sounder baseball."