After assessing damage by the powerful storm the PGA Tour announced the final round would resume on Monday at 10:00 EDT (14:00 GMT).
"We just got so much rain and wind, we've got some bunker problems, we've got a lot of standing water. That is the main thing," Mark Russell, PGA Tour vice-president of rules and competitions, said. "It just got to the point where we weren't going to be able to get the golf course ready.
"They're going to go out now and work till dark and then do the same thing at daybreak and try to get ready to play."
Woods had rolled in an 11-foot birdie putt on the second hole to open up a three-shot cushion when warning horns were sounded to evacuate the course, sending spectators and players running for cover.
Heavy rains and violent winds, reported at over 50 mph, soon followed, ripping branches from trees, cutting off power and turning Bay Hill into one massive water hazard.
"We didn't get in much," said Woods. "We got in two holes and hopefully the course will be drained and we can get after it tomorrow."
The 14-time major winner can reclaim the number one world ranking from Northern Ireland's Rory McIlroy with a victory at Bay Hill, where he has won seven times previously.
The PGA Tour has been plagued by weather woes this season.
Torrey Pines was forced to a Monday finish because of fog while high winds pushed the Tournament of Champions in Hawaii to a Tuesday conclusion.
"At least we got a little activity in today, so we're not completely stagnant," said Woods. "We've dealt with this before.
"We had that fog delay in San Diego, and this is part of playing outside. We've got to deal with conditions like this."
Officials reported no injuries but there was damage to several television installations and towers.
With the Sunday forecast calling for heavy rains, PGA officials were questioned on why they did not try to beat the storm by sending players off both the first and 10th tees.
"We talked about that (split tees) yesterday," admitted Russell. "We had a 50-50 chance, and we decided to try...we decided to play off one tee and the weather got us.
"We just got unlucky today. It's unfortunate, but there is nothing we can do about it."
It may take more than severe storm to keep Woods from taking an eighth Bay Hill title and reclaim the number one throne.
After a staggering 623 total weeks as number one, Woods has not sat atop the rankings for 29 months, a barren stretch that included two-and-half years without a PGA Tour win.
But Woods has been back in top form this season, having won twice in four starts with a chance to add a 77th PGA Tour victory to his resume on Monday and move within five of Sam Snead's record of 82.