Woods, who fired a 6-under 64 to lead at 9-under-par 131, missed the fairway right at the par-4 ninth, his 18th on Friday. He decided on a 9-iron, then hit that farther right and long.
The grandstands were also a factor as a 'temporary moveable obstruction,' and Woods dropped almost 100 yards from the hole near the clubhouse. He pitched to 30 feet and nearly holed the improbable par putt, but settled for a bogey.
All totaled, the final hole took the group, which included Paul McGinley, who hit it into the gallery, almost 45 minutes to complete the hole.
'At the end of the day, we operated off a temporary moveable obstruction rule,' said Mike Shea, a rules official. 'We knew the facts. It was due to the fact that the ball was picked up by an outside agency, that was one rule and the grandstand. It was all according to the rules of golf.'
For Woods, it was unlike anything he's experienced.
'That was the creme de la creme,' said Woods, who has won this tournament four times. 'I don't know how that ball wasn't out of bounds, first of all. Let's just say I hit a 9-iron a little too far.'
Davis Love III nearly made a birdie at the ninth from behind a tree, but settled for par. He posted a 5-under 65 on Friday and is alone in second place at minus-8.
Jim Furyk aced the par-315th en route to a 5-under 65 in the second round. He is tied for third place with overnight leader Adam Scott, who shot a 71, at 6-under-par 134.
While mostly everyone will talk about the strangeness involving the ninth hole, Woods played an unbelievable round on Friday.
The No. 1 player in the world birdied his first two holes, then made an 8-foot birdie putt at the 12th. Woods collected his fourth birdie in a row at 13 when he cashed in from 9 feet.
'I hit it well starting out,' acknowledged Woods, who has won his last three starts, including the British Open and PGA Championship. 'On top of that, I made some nice putts.'
Woods was one ahead when he made the turn after five consecutive pars. On the second nine, Woods started off the same way he began his second round.
He rolled in a 17-foot birdie putt at the first hole to reach 8-under par for the championship. At the par-5 second, Woods converted a 6-foot birdie putt to get into double figures at 10-under par, which was good for a three-shot lead.
Woods parred three, then sank a 10-footer for birdie at four. He struggled with his driver on some holes, but saved pars. At the seventh, Woods hit a 6-iron to 10 feet, but missed the birdie chance.
Then came the insanity at nine, but also the 36-hole lead.
'I'm happy to shoot a 64 out here on this golf course,' said Woods. 'I'm right there in position going into the weekend.'
Love traded three birdies and two bogeys over his first five holes, which were on the back nine at Firestone. He birdied the long, par-5 16th to make the turn in 33.
The 1997 PGA Champion, who was passed over this week by Tom Lehman for a spot on the United States Ryder Cup team, birdied two, four and five to move to eight-under par.
At the ninth, after a long wait to sort out the Woods mess, Love drove into the left rough, right against a tree. He knocked his second to seven feet, but missed his chance to tie for the lead.
Love now has a date in the final pairing with Woods on Saturday. That's not going to be an easy chore considering how well Woods is playing at the moment.
'I think you have to play very, very well,' said Love. 'He's obviously got a lot of confidence. You have to go out with a lot of confidence and block him out.'
Kevin Stadler (67), Lucas Glover (69) and Ernie Els (67) are knotted in fifth place at 5-under-par 135. Luke Donald shot a 1-under 69 and is alone in eighth place at minus-4.
Stewart Cink, who was named to the American team by Lehman on Monday, carded a 3-under 67 and is tied for ninth place with Robert Gamez, who shot the same number on Friday. The pair is knotted at 3-under-par 137.
Reigning Masters champion Phil Mickelson has struggled all week. He posted his second consecutive 4-over 74 and is part of a group tied for 68th at plus-8.