The world number two's mission this week was to play himself into form ahead of the Masters, and Friday's five-under-par 67 indicated he is back in the old groove, albeit with his new equipment.
The lowest round of the day briefly lifted McIlroy to one shot off the lead, which stood at six under, before late finisher Billy Horschel made back-to-back birdies at 17 and 18 to reach eight under after 36 holes.
But McIlroy, three shots back heading into the weekend in a six-player tie for fourth place, was just delighted to be back near the top of a leaderboard, having struggled this season.
He has seemed to have a hard time adapting to new equipment, and the form which brought him five wins in 2012, including a second major at the US PGA Championship, has been largely absent.
But in San Antonio his fortunes might on the turn, with McIlroy now hunting a trophy ahead of next week's major at Augusta.
"I'm looking forward to getting into contention. I haven't really been in contention this year and it'll be nice to get in the mix," the Northern Irishman said.
"I want to play well and know if I play well I'll have a great chance to win."
He said of his third round: "I knew the conditions were good and you had to take advantage of it.
"I played solid, I drove the ball well, hit quite a lot of greens, and made some nice putts coming in.
"It gets me in a good position going into the weekend.
"I turned in one under par and felt I was playing better than that."
A run of three birdies from 16 to 18 reassured McIlroy, and the challenge will be to shoot another low round on Saturday.
"I think I was rewarded for my patience out there," he said.
"It was a great way to finish and it'll make dinner taste nicer and give me a few more hours in bed.
"I'm feeling comfortable with my game.
"I definitely feel like I made the right decision to come here, and even if I hadn't been in this position and have been a few shots back I'd still feel the same way."
American Horschel leads from compatriots Charley Hoffman and Daniel Summerhays and Australian Steven Bowditch, all on six under.
As McIlroy ascended the leaderboard, he passed Padraig Harrington going the other way.
Dubliner Harrington had been four under after the opening round, just one off the lead, but at one stage in his second 18 holes he slipped back to one under. Starting on the back nine, he dropped shots at 11, 13 and 17 before repairing much of the damage on the front nine, with birdies at the sixth and ninth lifting him to a 73 and a healthier three under.
Scotland's Martin Laird was also three under after a 71, with Englishmen Brian Davis and David Lynn steady on two under after their respective rounds of 72 and 70. Ireland's Shane Lowry also carded a 72 to be two under through 36 holes.
Ian Poulter and Charl Schwartzel just made the cut at one over after shooting rounds of 75 and 73 respectively.