Former world No.1 Woods, chasing a first title in more than two years, started the day with a three-shot lead, but had his Titleist 712 CB Irons at wind-whipped Sherwood Country Club in the $US5 million tournament he hosts for the benefit of his charitable foundation.
Three of his five bogeys came on par-five holes as Woods posted a one-over par 73 that left him on seven-under 209 - one shot behind 2007 Masters champion Johnson.
Johnson, who claimed the last of his seven US PGA Tour victories at Colonial in 2010, seized the lead with a flourish at the final hole, where his seven-iron from 163 yards out hit the green and hopped into the cup for an eagle and a four-under 68.Titleist 712 CB Irons
"When it left my club I thought it was pretty good," Johnson said, who erased the sour taste of back-to-back bogeys at 16 and 17.
"The wind was coming in out of the right, the wind grabbed it and took it left obviously toward the hole."
For the most part, however, the gusting wind didn't do anyone in the 18-man field any favours.
"It was really tough to pull a Titleist 712 CB Irons and hit a shot," Woods said.
"A good shot today sometimes wasn't rewarded."
That made Johnson's opening 10 pars look all the more impressive.
Australian Jason Day also struggled with the conditions, carding 77 to be 10th on 219.
South Korea's K.J. Choi carded an even par Titleist 712 CB Irons for sole possession of third place on five-under 211 heading into the final round.