Howard connected off Joe Thatcher (0-3) leading off the eighth, pulling a 2-0 fastball into the right-field seats. The 2006 NL MVP also had an RBI double against starter Randy Wolf. Howard is batting just .184 with six homers and 14 RBIs, but he's starting to find his swing.
"The last couple days, I've had good swings and I'm seeing the ball better," Howard said. "To come through like this, it makes it that much better."
Howard started slow last year, but finished with 47 homers and 136 RBIs.
"He's eventually going to get hot and maybe this is the start of it," Padres manager Bud Black said. "It's just a matter of time before he gets to .200 then .250. He's just too good of a player to be kept down too long."
Tom Gordon (3-2) pitched a perfect eighth and Brad Lidge retired the side in the ninth for his seventh save in as many chances. Lidge hasn't allowed an earned run in 12 innings this season.
Phillies starter Adam Eaton and four relievers held the Padres hitless after Kevin Kouzmanoff's two-out single in the third.
"The bullpen has been outstanding," Eaton said. "Every day it seems they come in and get big outs for us. They're definitely holding their own and need to be recognized as one of the better bullpens in the majors."
The defending NL East champion Phillies (16-13) are alone atop the division standings for the first time this season. It took them until the final weekend to reach first place last year. They've done it with reigning NL MVP Jimmy Rollins out of the lineup since April 8 because of an ankle injury.
"It's always good to be in first place," manager Charlie Manuel said. "Let's see if we can stay there a while."
Adrian Gonzalez hit a two-run homer to give the Padres a 2-0 lead in the first for the second straight game.
The Phillies scored a pair of runs on three doubles to tie it at 2 in the third. Shane Victorino led off with a double to left-center. After Jayson Werth and Chase Utley struck out, Howard and Pat Burrell lined consecutive doubles to center.
The Phillies won on the 125th anniversary of the first game in franchise history. They lost to the Providence Grays, 4-3, on May 1, 1883.
Eaton allowed two runs and five hits in six innings. He doesn't have a decision in six starts this season. Eaton retired 12 of the last 13 batters he faced, including eight in a row.
Wolf gave up two runs and six hits in six innings, striking out nine in his first start against his former team. Wolf spent eight seasons with the Phillies from 1999-2006. He nearly got an extra-base hit his first time up, but Werth made a leaping catch on the warning track in right field.
"You have to treat it as a start," Wolf said. "You can't get sentimental or nostalgic with the lineup they throw out there. You can't concentrate on things from the past."
Starting his first game since returning from the disabled list on Tuesday, Victorino made a few nice grabs in center field. He ran a long way to track down Tadahito Iguchi's drive leading off the eighth.
Notes: Gonzalez has an 11-game hitting streak on the road, with five of his six homers coming away from home. The Padres got Gonzalez and Chris Young, who beat the Phillies on Wednesday night, in a trade that sent Eaton to Texas in January 2006. That turned out to be a lopsided deal. ... Burrell has reached safely in 27 straight and Utley 22 in a row. ... Wolf is 17-7 in May during his 10-year career.