Mickelson's management issued a written statement saying the San Diego resident decided late Friday to drop out of the tournament because of muscle pain in his back.
Mickelson was eight strokes off the lead Friday and faced 36 holes on the South Course, considered the more difficult of the two courses at seaside Torrey Pines.
CBSSports.com said Mickelson had indicated earlier in the week that he would not risk aggravating his aching back or altering his swing if he was not in contention.
Tiger Woods soldiered on Saturday after making the cut despite being tied for 70th place after Friday's round.
Members of Congress to keep receiving porn magazine
Putin thinks Obama would save him if he were drowning