Flesch, who has 12 top-10s to his credit this season but no wins, fired a 7-under-par 65 on the Magnolia course in Lake Buena Vista, Fla., to take a two-shot lead over the defending champion entering the weekend.
Flesch and Woods each carded 9-under-par 63s on Thursday, but Flesch bettered Tiger on Friday, 65 to 67.
Duffy Waldorf, playing the Palm course, shot a 6-under-par 66 to tie Carlos Franco for third place at 13-under-par. Franco, who is 28th on the money list, also shot 66, though he did so on the Magnolia course. Jeff Sluman is four shots off the lead at 12-under-par, after shooting a second-round 64 on the Palm course.
Flesch's day began with a birdie at the par-5 10th and ended with another at the par-4 9th. For the day, the left-hander carded seven birdies to nary a bogey. The 1998 PGA Tour Rookie of the Year has recorded 17 birdies and one bogey through two rounds.
'As well as I played yesterday, I expected to play well today,' said Flesch, who hit 16 of 18 greens in regulation on Friday. 'I can't go out and protect anything. I have to go out there and perform or I'll get run by.'
For Tiger, it was a day of missed opportunities. Woods managed a bogey-free 67, but parred three of the four par-5s.
'Interesting day,' Tiger quipped. 'I kept myself in there, made a few putts. I need to hit the ball close to the flag tomorrow and make a few more putts like I did yesterday.'
This is the final opportunity for players to qualify for next week's Tour Championship. The top-30 gain entrance into the $5-million event. Rocco Mediate, who entered the week in 30th position, missed the NCR cut by three strokes.
Mediate probably won't be making the trip to the East Lake Golf Club in Atlanta, Ga., as both Scott Hoch (No. 31) and Chris Perry (No. 32) made the cut. Hoch and Perry stand at 6-under and 8-under-par, respectively.