McIlroy, who lost to Peter Uihlein on day one, never trailed in the contest and was three up with three to play, but still had to hole from 6ft for par on the 17th to avoid being taken down the last.
The 2015 champion could still win the group by beating Brian Harman today, although he would face a play-off with Uihlein if the American beats the already eliminated Colombian Vegas.
McIlroy came into the week on the back of his win in the Arnold Palmer Invitational on Sunday and told Sky Sports: “I could have done with that extra day. You win on a Sunday and usually you’re teeing it back up on a Thursday but you have to start on a Wednesday here.
“I did feel a bit flat on Wednesday coming back out here. I don’t want to use that as an excuse, Peter played great, but there’s sometimes a little bit of a hangover and I was tired.
“This is my sixth week out of seven as well so I’m looking forward to hopefully getting through to the weekend here but putting the clubs away for a couple of days before getting ready for Augusta.”
World number one and defending champion Dustin Johnson crashed out with a game to play after suffering his second straight defeat.
Johnson never trailed at any point in his seven matches last year as he became the first player to win all four World Golf Championship titles.
But the 33-year-old lost to Austria’s Bernd Wiesberger on the opening day at Austin Country Club and was again out of sorts in a 4&3 defeat to Canada’s Adam Hadwin yesterday which guarantees he cannot qualify for the knockout stages.
An eagle on the sixth and a birdie from 35ft on the ninth gave Hadwin command of the match and Johnson’s hopes effectively sank when he hit two balls into the water on the short par-four 13th.
European number one Tommy Fleetwood had earlier bounced back from an “awful” opening defeat to Ian Poulter to cruise to a 7&6 victory over American Kevin Chappell.
The destiny of Group 9 is still in Poulter’s hands after he beat Berger 2&1 to maintain his 100% record. “If last year taught me anything it’s that every point counts so there’s no point sitting and wallowing or thinking I’ll just have tomorrow off and not be bothered about winning,” added Fleetwood, who won the 2017 Race to Dubai by 58,821 points from Justin Rose. “If I can win tomorrow we’ll see what happens.”
Ryder Cup partners Jordan Spieth and Patrick Reed will go head-to-head today to decide the winner of Group 4, Spieth beating Li Haotong 4&2 and Reed defeating former Masters champion Charl Schwartzel on the 18th.