Garcia, the 2001 and 2004 winner at Westchester Country Club, opened with a 2-over 73 and was 3 over for the tournament when he pulled out.
'I hurt my back Wednesday practicing and playing in the pro-am and struggled with it the last two days,' Garcia said. 'After nine holes today, I wasn't able to continue. I regret having to withdraw.'
The Spanish star expects to play next week in the U.S. Open at nearby Winged Foot.
'I hope to rest and be at or near 100 percent next week at the U.S. Open,' he said.
Rocco Mediate, tied for fifth after a first-round 68, also withdrew during the round because of a back injury. He opened with a birdie and made double bogeys on Nos. 2 and 3 before walking off the course.
Jim Furyk withdrew Wednesday because of a back injury.