"It wasn't so much what I didn't do as what Myers did do," Johnson said. "He shut us down. He pitched extremely well."
Myers (5-3) allowed two runs in 6 2/3 innings and Aaron Rowand had an RBI double, helping the Phillies even their record at 35-35 with their second straight win after a six-game losing streak.
Johnson (8-6) had his second encouraging outing in a row and Jason Giambi homered for the struggling Yankees, who have lost three straight and eight of 11.
"Right now we can't afford to allow little things to happen," Yankees manager Joe Torre said. "We have to be as tight as can be with pitching and defense because we're scuffling."
"When you see a lineup like that, you know you have to bear down more," Myers said.
Johnson allowed three runs and five hits in seven innings. He dropped his appeal of a five-game suspension for throwing at Cleveland's Eduardo Perez last week and will begin serving on Tuesday. Johnson's next start will likely be next Monday against Atlanta.
Burrell's two-run double in the fourth inning put the Phillies ahead 2-1. With one out, Shane Victorino reached on an infield single and went to second on second baseman Robinson Cano's throwing error. Chase Utley walked and Burrell lined a shot into the left-field corner to score both runners.
Phillies second baseman Abraham Nunez kept it at 2-1 with an outstanding defensive play on Johnson's hard grounder up the middle to end the fifth. With a runner on second, Nunez dove to his right, made the backhanded stop and easily threw out Johnson.
"That was the play of the game," Torre said.
Rowand's two-out RBI double in the sixth made it 3-1.
Myers left after walking Alex Rodriguez to load the bases in the seventh. Rheal Cormier came in and Jorge Posada's infield single drove in a run to cut it to 3-2. Shortstop Jimmy Rollins made a diving play on the one-hopper in the third-base hole to prevent the tying run from scoring.
Cormier then retired Cano on a grounder to second base to end the inning.
The Phillies added an insurance run in the eighth against Kyle Farnsworth. With two outs and the bases loaded, David Bell struck out but reached on a wild pitch, allowing Rollins to score. Farnsworth, in his first action since back spasms forced him out Friday night, hit Rollins in the back of his helmet with a 95 mph fastball leading off the inning.
"Any time you play the Yankees, it's fun to beat them," Rollins said. "It seems like you concentrate more. They bring out the best in you."
Giambi ripped a shot into the second deck in right field for his 19th homer in the fourth inning, giving the Yankees a 1-0 lead.
For the second consecutive start, Johnson looked more like the pitcher who has dominated batters for nearly two decades than the one whose ERA has been stuck above 5.00 most of the season. The 42-year-old left-hander had seven strikeouts and two walks.
"I've moved past that," Johnson said. "I'm not as done as some people think I am."
Myers had his best outing since June 4. He didn't allow more than three earned runs in any of his first 12 starts but couldn't get past the third inning in his last two. He gave up 11 earned runs and 16 hits in 5 2/3 innings in those two starts.
A sellout crowd of 44,747 included plenty of New Yorkers wearing Yankees jerseys, but the Phillies fans drowned out the noise by cheering loudly for the home team. When the Mets swept a three-game series in Philadelphia last week, it sounded more like Shea Stadium at Citizens Bank Park.
Giambi was 3-for-19 before he homered. ... Myers reached double digits in strikeouts for the sixth time in his career and first time since fanning a career-best 12 against Washington last Oct. 1. ... Phillies first baseman Ryan Howard, who leads the team with 23 homers and 59 RBI, and right fielder Bobby Abreu had the night off against Johnson. ... The Phillies improved to 18-21 at home, the worst record at home for a non-losing team. ... Rodriguez robbed Burrell of extra bases with a diving, backhanded play on a sharp grounder down the third-base line with runners on first and second in the eighth. ... Gordon reached 20 saves for the third time in his career and first time since 2001, the last year he was a full-time closer.