That decision did not please regular starting catcher Jorge Posada, who on Tuesday said: "I just hope we win that game. That's all I've got to say."
And Posada's tone and demeanor made it clear he was not happy.
Burnett, speaking with reporters in the Yankees' dugout before Wednesday's opening game of the American League Division Series, said the move was manager Joe Girardi's call, not his -- and that his relationship with Posada is fine.
Although Burnett pitched better down the stretch with Molina behind the plate, Molina is not nearly as productive a hitter as Posada.
"It was the manager's decision, I had no part in it," Burnett said. "I've thrown good to both [catchers]. My good games, I'm right. My bad games, it's not the catcher, it's me ... When I'm good, it doesn't matter which one is behind the plate."
If there's an issue between Posada and Burnett, it seems to go back to Aug. 22, when the Boston Red Sox roughed up Burnett for nine runs in five innings, including three home runs, in a 14-1 rout.
After Burnett gave up a home run to David Ortiz in the fifth inning, he was caught on camera saying, "Why?" to himself. It was not initially clear if he was questioning himself or Posada, who caught that game.
Since then, Burnett has made eight starts, with Posada catching only one. With Molina catching, he was 3-1 with a 2.92 ERA in his final six starts.
"It's making me out to be the bad guy again," Burnett said Wednesday. "It comes down to Boston when I said, 'Why, why, why?' But over my career, I've done that a handful of times. If you ask guys I've played with, I don't show guys up.
"And obviously Jorge's upset. He's a big part of this team. He's a leader on and off the field and hopefully his mind will be right to get in there and get a pinch hit when the time comes," he said.
Girardi said he didn't expect Posada to be excited about Molina catching Burnett in the postseason.
"When I played here, we split guys during the playoffs," Girardi said Thursday. "Of course, you want to play every day. I wouldn't want a catcher who didn't want to play every day. That would bother me inside if the guy didn't want to play every day."
Posada started Game 1 against the Minnesota Twins, going 1-for-4 with a strikeout and two passed balls in the Yankees' 7-2 win.
He batted .285 with 22 home runs this season; Molina batted .217 with 30 hits in 138 at-bats.
"I can't do nothing about it," Posada said. "Just sit and watch the ballgame."
Information from The Associated Press was used in this report.