Mickelson, who opened the tournament Thursday with a three-under-par 69 on the North Course, struggled to keep pace with the contenders Friday as he shot a one-over 73 in the second round on the tougher South Course.
Although he reported having some pain in his back following the round, he was hoping to at least attempt to play in the third round on Saturday.
A few hours after his round, though, the PGA Tour took to Twitter to inform fans that Mickelson had withdrawn.
Phil Mickelson withdrew from the @FarmersInsOpen several hours after his 2nd round Friday, due to muscle pain in his lower back.— PGA TOUR Media (@PGATOURmedia) January 25, 2014
Mickelson, who does not have a history of back problems, reached the midway point of the tournament eight shots behind leader Jordan Spieth.
“I love this tournament and I want to play here," Mickelson said after his round, when he still had hopes of continuing to play this weekend. "I love playing in San Diego, and this is a place where I grew up playing, so I really want to play."
But Mickelson, who said he felt the back pain last week when he was runner-up at the Abu Dhabi Championship, felt pain in the first round and changed his swing on Friday to try to lessen the discomfort. He mentioned on more than one occasion to reporters after his second round that he didn't want to form bad habits.
“I have the entire year," Mickelson said. "I've got majors coming up. I've got other tournaments coming up and I don't want to get in bad habits. My game is pretty sharp getting ready to start the year and I could tell I'm making terrible swings out there relative to the way I've been swinging."