"We know what we're doing with him, but he seems to get us almost every series," Braves manager Bobby Cox said. "We make mistakes."
Howard homered twice, Jimmy Rollins hit a three-run shot, and the Philadelphia Phillies overcame a shortened start by rookie J.A. Happ to end Atlanta's seven-game winning streak with a 9-4 victory Friday night.
Philadelphia, which has won six straight, stopped the Braves' longest stretch of consecutive victories since July 2006, dropping Atlanta 8 1/2 games back in the National League East and hurting their fading wild-card chances.
Howard's 39th and 40th homers came off Tim Hudson (1-1), who gave up six hits, three runs and one walk with three strikeouts in seven innings.
Rookie Boone Logan, the second of four Atlanta relievers to follow Hudson, made just three pitches before hitting Howard with a 95 mph fastball in the eighth.
"It wasn't that I got hit," Howard said. "It was that I got hit in the same spot [Thursday against Washington]. No, I'm sure he didn't try to hit me, not with an 0-2 count and runners at second and third."
Happ, making his first start since Sept. 2 because of a strained oblique, left after three innings and did not earn a decision. The Phillies announced his departure was for "precautionary reasons" after the left-hander allowed five hits, one run, no walks and struck out one.
Happ doesn't know if he will make his next scheduled start.
"I'd thrown  pitches but I felt good," Happ said. "I was throwing quite a few changeups. I was throwing them for strikes. I had a good curve."
Kyle Kendrick (2-1) won his second consecutive appearance with four scoreless innings. Allowing four hits with no walks or strikeouts, Kendrick began the fourth with a 2-1 lead courtesy of Howard's two-run shot in the fourth.
Jayson Werth gave the Phillies a 5-1 lead with a two-run single in the eighth.
Howard made it 3-1 in the sixth, giving him six multihomer games this season and 23 overall to tie Chuck Klein for second-most on the Phillies' career list.
Happ stayed in the game after manager Charlie Manuel, pitching coach Rich Dubee and team trainer visited the mound in the third. Four pitches later, Martin Prado's 10th homer gave the Braves a 1-0 lead.
"He said he was OK, but he didn't have a lot on the ball," Manuel said. "He didn't have a lot on the ball."
Hudson, making his fifth start since returning from elbow ligament replacement surgery, retired first 10 batters he faced, allowing no hits or walks, before Francisco singled in the fourth.
Howard raised his career average to .353 with five homers in 34 career at-bats against Hudson.
"I couldn't quite keep the big fellow in the park tonight," Hudson said. "I'm scratching my head with this guy. I mean, it seems like every time I pitch against these guys, he takes me deep. Im obviously not the only guy he does that to. It's one of those things that if I make a mistake, he don't miss it."
Facing Atlanta pitching in a career that spans nearly six full seasons, the 2006 NL MVP is now hitting .342 with 31 homers and 85 RBIs in 295 career at-bats.
"It just happens," Howard said. "I like Atlanta. Good food."
Cox pulled SS Yunel Escobar for failing to run out a grounder in the first. Omar Infante took Escobar's place to begin the top of the third. ... Phillies C Carlos Ruiz left after five innings because of a left wrist strain. Paul Bako took his place. ... Braves C McCann threw out two runners trying to steal third, Ben Francisco in the sixth and Howard in the eighth. ... Philadelphia LF Raul Ibanez threw out Matt Diaz at the plate to end the second. Diaz was trying to score from second on Hudson's single. ... Braves 3B Chipper Jones was a late addition to Atlanta's lineup, returning after missing the last four games with a strained groin. He went 1 for 4. ... Philadelphia CF Shane Victorino was "feeling under the weather," according to Manuel, and was held out of the lineup. Francisco started in his place. ... Philadelphia improved to 23-13 in its last 36 games with Atlanta.