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.
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. Right fielder Jeff Francoeur, their most productive hitter of late, sat out with a torn ligament in his left thumb. New York said he is day-to-day.
Francoeur, obtained in a trade with the Braves last month, got hurt Sunday while making a diving catch. X-rays were negative, but his thumb swelled up afterward and he went to the hospital Monday for an MRI that revealed the tear.
Cory Sullivan started in right for the Mets.
Bobby Parnell (3-6) made his fourth start for New York 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. Howard drove a 2-2 delivery to the opposite field, putting Philadelphia up 3-0.
It was the third time in two days that the Phillies hit a three-run homer in the first inning. Jayson Werth and Carlos Ruiz connected Sunday off Oliver Perez.
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.
The big slugger had a chance to do more damage in the sixth but he struck out with the bases loaded against Ken Takahashi, leaving Howard with 34 homers and 104 RBIs.
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.
Gary Sheffield blooped a one-out triple to right and scored Tatis' long sacrifice fly, but Lee settled in from there.
Raul Ibanez added an RBI double in the ninth off Pedro Feliciano. Chan Ho Park and Brad Lidge each worked a perfect inning to finish it for the Phillies.
NOTES: 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. ... The Mets recalled Takahashi from Triple-A Buffalo and optioned LHP Pat Misch to their top farm club. Takahashi relieved Parnell to start the sixth. ... New York RHP Brandon Moore pitched a seven-inning no-hitter for Class-A Brooklyn in the opener of a doubleheader at Aberdeen on Sunday. The Mets, who began play in 1962, have never thrown a no-hitter. ... The Phillies are 24-13 in day games, the best mark in the National League.