"Your heart wants to do it," Girardi said, "but you head tells you that you need to make a change."
Chamberlain gave up one run on four hits in 5 2-3 innings in his fourth start. He also helped prevent a run with his catcher's skills, blocking home plate to make a tag.
Then Chamberlain's former mates in the bullpen showed they're doing just fine without him, holding the Padres scoreless the rest of the way.
Another key hit from Alex Rodriguez drove in the go-ahead run.
The Yankees ran their way to scoring opportunities, setting up both their runs with stolen bases. San Diego, meanwhile, was running its way into outs, as Adrian Gonzalez was thrown out at home plate twice in the first four innings.
New York extended its longest winning streak of the season to seven and improved to seven games above .500 for the first time this year. The Padres have dropped five of six.
Rodriguez, who homered in the previous four games, drove in Derek Jeter with a single in the sixth off Josh Banks (2-1). Jeter had singled, stolen second and moved up on Bobby Abreu's grounder to first.
The Yankees got their first run without a hit to tie the score an inning earlier. Melky Cabrera walked with one out, then stole second and third. Jose Molina drove him in with a sacrifice fly.
"That means we can play small ball, too," Molina said. "We're not waiting for the home run all the time."
New York stole four bases for the second straight game. Two of them led to runs in Wednesday's 8-5 win.
"What the Yankees do as far as base stealing, they do a good job of identifying the pitcher. They take advantage of that slowness to the plate or the higher leg kick," Padres manager Bud Black said. "We have to quicken our time to home plate."
For the first time, Chamberlain wasn't on a strict pitch count, but Girardi said beforehand he didn't want the right-hander to throw many more than 100. He wasn't kidding.
After Chamberlain struck out Chase Headley with his 100th pitch, Girardi popped out of the dugout to remove him.
The fans voiced their disapproval, but Girardi wasn't going to risk a 10-pitch at-bat. He said he told Chamberlain, "I understand you don't want to come out. You can be upset about it. That's how I want you to be."
Chamberlain got a standing ovation as he left the field.
"I understand it's June," he said afterward, "and this is my first time getting to 100 in the big leagues."
Jose Veras (2-0) came in and pitched 1 1-3 innings to earn the win. Kyle Farnsworth worked the eighth to set up Rivera, who struck out the side in the ninth for his 20th save in 20 chances. Rivera didn't get his 20th save last season until Aug. 18.
"Everyone is giving us important innings," Girardi said of his bullpen.
Girardi would rather his pitchers not block the plate, as Chamberlain did in the second. But he appreciated the competitiveness.
With one out, Chamberlain's pitch in the dirt got away from Molina, and Gonzalez took off. The catcher quickly tracked the ball down and threw to Chamberlain.
"I was a catcher until I was a junior in high school," Chamberlain said. "So it brought back some memories. I guess it's like riding a bike."
Molina joked, "That was kind of ugly." He added in admiration, "That means he's a tough guy."
Black said Gonzalez expected the ball to roll farther, but the grass is thicker behind home plate at Yankee Stadium than at other parks.
The inning had started with the Padres loading the bases with no outs, but Chamberlain wriggled out of the jam with the tag-out sandwiched between two strikeouts.
With one out in the fourth, Gonzalez tried to score on Scott Hairston's grounder to third and was thrown out by Rodriguez.
Tony Clark drove in Brian Giles with a ground-rule double in the fourth for the Padres' lone run.
It was the sixth time in nine games that New York pitchers allowed no more than one run. The Yankees have won nine times this year when scoring three runs or fewer; they did that six times all last season.
"Look, without guys like Joba, you can't win championships," Rodriguez said. "That's just the bottom line. We need him in the starting rotation."
