PALM BEACH GARDENS, March 1, 2014 (AFP) - McIlroy fired four birdies against three bogeys at PGA National to stand on 12-under par 198, two strokes ahead of American Russell Henley.
Scotsman Russell Knox was third on 201 with Venezuelan Jhonattan Vegas on 202 and England's Luke Donald, Australian Stuart Appleby and Americans Ryan Palmer and Keegan Bradley on 203.
McIlroy could join Jack Nicklaus, Mark Calcavecchia and Johnny Miller as the only repeat winners of the $6 million event, the 24-year-old Northern Irishman having taken the title in 2012 to become world number one for the first time.
"I feel comfortable with where my game is," McIlroy said. "I thought 69 in the conditions I had today was a pretty good score."
Woods, meanwhile, made seven birdies against two bogeys on his way to a five-under 65, his low round of the year, to stand on 205, seven strokes off the pace in a share of 17th after only making the cut on the number.
"I struck the ball well and made some putts," Woods said.
McIlroy, who walked off the course here last year with claims of a toothache but later apologized, solved tricky breezes and could take a wire-to-wire victory near his South Florida home with his parents and tennis-star fiancee Caroline Wozniacki watching.
"It was a little more difficult for sure," McIlroy said. "The wind was coming from a slightly different direction which made the last few holes play quite tough. That's about as tough as they play.
"You can't get away with anything out here. You have to be in control of your golf ball and for the most part I have been this week."
Two-time major champion McIlroy teed off only one stroke ahead of playing partner Brendon de Jonge and each birdied the first and par-5 third holes, but Zimbabwe's de Jonge fell two back with a bogey at the fourth.
De Jonge took a double bogey at the sixth but McIlroy made bogeys at the sixth and par-3 seventh. De Jonge birdied eight but a bogey at nine and a double bogey at 11 heralded a back-nine collapse, a bogey-bogey finish taking him to a 76 and eight shots off the lead.
McIlroy sank a five-foot birdie at 12 to move four clear of the field and followed a bogey at 14 with a nine-foot birdie putt at 16.
Henley, who had 10 pars and a bogey to start, birdied 12 and reached 10-under with a 150-yard eagle shot from the fairway at the par-4 14th.
"I couldn't have hit it any better," Henley said. "It was a pretty cool feeling."
Henley missed a seven-foot par putt at 15 but answered with a 48-foot birdie at the par-3 17th, the fast-rolling ball popping into the air as it hit the hole before falling into the cup.
Woods enjoyed his finest round of the year after missing the secondary cut at Torrey Pines and sharing 41st at Dubai.
"It's going to turn around," Woods said. "We are all going to have hot spells and we're going to have cold spells, especially the longer we stay out here. I've had situations where it just seems like no matter what you do, nothing really goes your way."
Woods, in the second group out, opened with a 15-foot birdie, went over the green on his way to a bogey at the fourth, then birdied the par-3 fifth from 38 feet and the par-3 seventh from 25 feet.
"I had good feel today," Woods said.
Woods sank an eight-foot birdie putt at 10, chipped in from beyond 50 feet at the 12th and followed with a 15-foot birdie at 14 and a five-footer at 15.
Leading scores on Saturday after the third round of the $6 million US PGA Tour Honda Classic (USA unless noted, par-70):
198 - Rory McIlroy (NIR) 63-66-69
200 - Russell Henley 64-68-68
201 - Russell Knox (SCO) 70-63-68
202 - Jhonattan Vegas (VEN) 70-66-66
203 - Stuart Appleby (AUS) 69-69-65, Keegan Bradley 69-68-66, Luke Donald (ENG) 67-68-68, Ryan Palmer 68-66-69
204 - Matt Every 66-73-65, Cameron Tringale 69-69-66, Nicholas Thompson 68-70-66, Ted Potter 71-66-67, Billy Hurley 70-67-67, Rory Sabbatini (RSA) 65-71-68, Will MacKenzie 67-68-69, Daniel Summerhays 70-65-69
205 - Tiger Woods 71-69-65, Luke Guthrie 67-73-65, Brian Stuard 72-68-65, Freddie Jacobson (SWE) 69-69-67, Zach Johnson 67-70-68, David Lingmerth (SWE) 69-68-68, Thomas Bjorn (DEN) 69-66-70
206 - Tim Wilkinson (NZL) 70-69-67, Hudson Swafford 67-71-68, Tyrone Van Aswegan (RSA) 67-71-68, George McNeil 70-67-69, Stewart Cink 69-68-69, Brendan Steele 69-66-71, Jason Kokrak 70-66-70, Derek Ernest 66-69-71, Jamie Donaldson (WAL) 65-69-72, Lee Westwood (ENG) 68-65-73, Brendon de Jonge (ZIM) 66-64-76