Woods, who shot four-under-par 68 on the South Course in his opening round, shot four-under 32 on his front nine Friday and was eight-under overall as he made the turn.
Woods was tied at one point with Charles Howell III for the lead but Howell fell to seven-under when he made bogey five on the South Course's par-four 10th hole, giving Woods the solo lead.
Woods started play on the North Course's 10th tee Friday morning and he went birdie-eagle on the 17th and 18th holes. Woods also birdied the par-five 14th hole.
Woods has won the PGA event at Torrey Pines six times and also claimed the 2008 U.S. Open on the course. He holds the South Course record of 62, which he set in 1999.