Howard homered twice and drove in five runs, Lee won his eighth straight start and Philadelphia beat the New York Mets 6-2 on Monday.
Lee (5-0) did not allow an earned run in seven innings, lowering his ERA with the Phillies to 0.68 in five outings since he was acquired in a July 29 trade with Cleveland. His record is 12-9 overall.
"He makes us real good," manager Charlie Manuel said. "We've got some top-notch left-handed pitchers. I kind of like that. Definitely the best rotation that we've had since I've been here."
New York's rotation took a hit after the game: Johan Santana was scratched from Tuesday night's scheduled start in Florida because of discomfort in his pitching elbow.
"He has not been throwing between starts for quite awhile. I would say since before the All-Star break. He has been pitching with this problem, but not with the level of discomfort he has now," manager Jerry Manuel said. "Now, it concerns him."
The ace left-hander will be examined Tuesday by Mets medical director Dr. David Altchek, and Nelson Figueroa will start against the Marlins.
One day after second baseman Eric Bruntlett became the second major leaguer to end a game with an unassisted triple play, the Phillies beat their injury-riddled rivals in more conventional fashion.
Lee, last year's AL Cy Young Award winner, yielded six hits and no walks against a light-hitting lineup that featured Fernando Tatis (six homers) in the cleanup spot. The left-hander struck out five.
"Whenever he's on the bump, you feel pretty confident," Howard said.
The Phillies said Lee became the first pitcher to win his first five starts with the team since Marty Bystrom in September 1980, according to research by the Elias Sports Bureau.
"It was already an unbelievable team before I got here. That's made it easy for me," Lee said. "It's been a pretty smooth transition."
Philadelphia took the final three in a four-game series and won for the 11th time in 13 games overall, increasing its NL East lead to seven games over idle Atlanta.
The defending World Series champions are 40-21 on the road, the best mark in the majors. They have won 14 of their last 20 away from home.
Incredibly, the fourth-place Mets received more bad injury news. In addition to Santana, right fielder Jeff Francoeur, the team's most productive hitter of late, sat out with a torn ligament in his left thumb. New York said he is day to day.
Bobby Parnell (3-6) made his fourth start for the Mets after spending the first four months of the season in the bullpen. Roughed up in his previous outing against Atlanta, the rookie right-hander got himself in trouble right away.
Parnell hit leadoff batter Shane Victorino with a 2-2 pitch and walked Chase Utley with one out. On an inside-out swing, Howard drove a 2-2 delivery to the opposite field, putting Philadelphia up 3-0.
"I told him one of these days if he ever gets strong, he's going to be a pretty good hitter," Charlie Manuel said, joking.
The home run also pushed Howard past 100 RBIs, giving him four straight seasons with at least 30 homers and 100 RBIs. The only other Phillies player to accomplish that was Hall of Famer Chuck Klein from 1929-32.
Howard added a two-run drive off Parnell in the third, sending a full-count pitch into the front row of the second deck in right for his 21st career multihomer game and fourth this season.
"I'm just scrambling a little to get back to my groove as a starter," said Parnell, who filled that role in the minors.
Angel Pagan scored on a wacky play leading off the bottom of the first. His routine popup to second was dropped by Utley, who then made a wild throw to second that allowed Pagan to circle the bases.
Utley was charged with two errors on the play. The previous day, Pagan led off the first inning with an inside-the-park homer.
Mets reliever Billy Wagner made his second appearance since returning sooner than expected from elbow ligament replacement surgery last September. The left-hander struck out two in a hitless eighth. ... Ruiz and Phillies SS Jimmy Rollins were rested. Rollins flied out as a pinch hitter in the ninth and stayed in the game. Bruntlett started at SS. ... RHP Brett Myers (hip surgery) was scheduled to pitch one inning in a rehab assignment for Class-A Lakewood.