Johnson withdrew Friday after playing the first nine holes at La Quinta Country Club.
The world's No. 8 player was the highest-ranked competitor in Palm Springs this week. He shot an even-par 72 on the Palmer Course on Thursday.
Johnson had arthroscopic surgery on his right knee in November, and he hadn't walked 18 holes until Thursday. He said his lower back in extremely stiff and painful.
Johnson also skipped the PGA Tour's first two events of the season in Hawaii, but he says he'll play the Farmers Insurance Open next week at Torrey Pines. He's a two-time winner at Pebble Beach.