Howard and Werth connected against Neal Cotts in the eighth to make it 5-1, and reliever J.C. Romero cut off a Cubs rally in the bottom half by striking out the side - including Geovany Soto with the bases loaded.
The NL Central-leading Cubs, who rallied to win Thursday and Friday, opened the bottom half of the eighth with consecutive singles from Ryan Theriot, Derrek Lee and Aramis Ramirez to trim the lead to 5-2.
Romero replaced starter Brett Myers and struck out pinch-hitters Reed Johnson and Ronny Cedeno before walking Kosuke Fukudome to load the bases. He then got a called third strike past Soto to end the threat.
Brad Lidge pitched a perfect ninth for his 32nd save in as many chances.
Myers (8-10) allowed 11 hits and two runs in seven-plus innings with no walks and eight strikeouts. He is 5-1 in eight starts since being recalled from the minors on July 20.
The 6-foot-4 right-hander didn't given up a run in his two previous starts and had his scoreless inning streak snapped at 17 when the Cubs got three straight singles from Mark DeRosa, Fukudome (a bunt) and Soto with one out in the second to take a 1-0 lead.
Ted Lilly (13-8) retired 12 straight before Werth led off the fifth with his 19th homer. Lilly lost another matchup with Werth in the sixth, surrendering a two-out single that scored Chase Utley easily and Howard on a nice slide around Soto.
Home plate umpire Chris Guccione, who was in the middle of a disputed call at first Friday, was involved in another in the fourth inning Saturday when the Cubs had runners at the corners. When Howard picked up Lilly's bunt down the first-base line and tried to tag him, Guccione initially ruled Lilly safe at first.
After Howard protested, crew chief and first base umpire Tim Welke met with Guccione and ruled Lilly was out - even though replays were inconclusive on whether Howard tagged him. Cubs manager Lou Piniella came out to argue after the call was reversed.
On Saturday, Guccione had called Howard out at first on a close play with runners also on the corners. Replays showed he beat the throw and if he'd been ruled safe, the Phils would have taken a seventh-inning lead in a game they eventually lost 3-2.
Notes: Werth is 9-for-17 with three homers and seven RBIs against the Cubs this season. ... Myers is 2-7 on the road this season. ... Ramirez's RBI single gave him 100 RBIs. ... Cubs ace Carlos Zambrano, who has just one win in his last five starts and failed to get past the fifth in two of them, has a tired arm. He will pitch the series finale Sunday. Zambrano went through a similar experience last season when he went winless in August and had a dropoff in velocity. "He doesn't have a sore arm and he doesn't have a dead arm. He might have a little bit of a tired arm. It's muscular," Piniella said. Zambrano said he'd eased up during his sessions between starts with more long tosses and said he has no pain and is OK. Zambrano bounced back last season to win four of his final five regular-season starts.