It was the first time Koepka and McIlroy had been paired in a final round, raising hopes of a day-long duel. But McIlroy missed a short birdie putt at the third hole from inside four feet and never recovered.
Tiger Woods rallied to defeat fellow American Patrick Cantlay 4&2 and Northern Irishman Rory McIlroy prevailed over England's Matthew Fitzpatrick by the same score. That put both in Saturday's round of 16.
Beaten 2&1 by Brandt Snedeker, Tiger Woods will need to defeat Patrick Cantlay on the final day of the round-robin phase at Austin Country Club and hope Aaron Wise can win against Snedeker in the other match to go through.
Tiger Woods fell behind fellow American Aaron Wise through 10 holes but battled back to seal the win when the 22-year-old missed a short putt on the 17th, handing the four-times Masters champion a 3 and 1 victory.