The golfer was seven under par and far from the lead when he chose to withdraw from the competition, which was his first start of the season.
The announcement came shortly before he was due to tee off in the third round.
At this time last year, Åberg was forced to withdraw from the competition in Torrey Pines with a stomach ailment.
The 26-year-old is the fourth player to be forced to withdraw from the PGA Tour event at La Quinta, with Luke Clanton, Rico Hoey and Nick Dunlap also withdrawing.
