Now, the Englishman holds a five-shot lead over the defending champion entering the third round of the Dubai Desert Classic.
Fisher shot a second consecutive 7-under-par 65 on Friday and is at 14 under halfway through the tournament. Woods struggled with his putting again and finished with 67 to stand at 9 under.
"It was kind of weird," Woods said. "I just didn't feel like I made many putts today. I was all around the hole and most of them were actually misreads."
Three-time Desert Classic winner Ernie Els climbed within two strokes of the lead with an eagle on the 13th hole, but didn't finish his round.
The second round was cut short because of darkness at Emirates Golf Club after a rare Dubai thunderstorm delayed play for more than two hours. Fisher held a four-stroke clubhouse lead over Peter Hanson and Graeme McDowell.
"I'm hitting the ball probably as good as I've ever hit it," said Fisher, who had eight birdies and a bogey. "It would be tough to have a third 65, but you know it's out there if you play well."
The Desert Classic is just the second tournament in which Fisher has been the leader - the first was the 2005 China Open.
The 26-year-old Englishman described how he'd spent his early years in awe of Woods. He said the closest contact he had with him was when he worked as a teenager on a driving range at the World Match Play Championship at Wentworth in England.
"I've never met him or spoke to him," he said.
WOMEN'S AUSTRALIAN OPEN: In Sydney, Australia, Karrie Webb shot 1-under-par 71 to take a one-stroke lead after two rounds of the tournament.
Webb, who trailed Sarah Kemp by one after the first round at Royal Sydney, moved to 6 under for the tournament.
She has a one-stroke lead over Taiwan's Wei Yun-jye, who also finished with 71. Australian Nikki Campbell carded 73 in the second round and is third, two behind Webb.
Webb, playing for the first time in two months, had three birdies and two bogeys.
"My distance control wasn't great," said Webb, who won five tournaments last year. "I didn't hit very well, that's why I'm pretty happy to get away with 1 under.
Ahn Sun-ju and Amy Yang are tied for fourth.