Lowry, who opened at Harbour Town Golf Links with a 6-under 65 after a 78-73 flameout at the Masters last week, knew conditions were worsening and jumped all over the course as quick as he could with birdies on the first and second holes before storms swept the island resort area.
After waiting out a delay of 3 hours, 43 minutes, Lowry played consistently enough to keep in front.
Trey Mullinax was a stroke behind after a 68. Top-ranked Dustin Johnson and Emiliano Grillo were 7 under after 67s.
Lowry was among 56 players who'll return Saturday morning to complete the second round before starting the third.
Mullinax, a shot behind when the round began, tied Lowry with a birdie on the 13th. But the Irishman countered moments later with a two-putt birdie on the 15th to take the lead.
Lowry opened with a 65 to take the first-round lead Thursday. The Irishman birdied his first two holes to get to 8 under before play was halted due to a strong storm system that had caused problems throughout the Southeast this week.
"This is one of those days when you look forward to getting back on the couch and watching the guys (in the afternoon) deal with it," said past RBC Heritage champion Matt Kuchar, a morning starter who finished before the delay. "It's one of those struggling days where you have gone through your own struggles and fun to watch your friends go through it."
Mullinax wouldn't have minded that, either. But instead he played into the fading light as the wind picked up over his final holes. He said he backed off twice on his five-footer on the 18th to finish with a par.
"It was probably blowing about 30 on that putt on that green so I had to back off," Mullinax said. "I didn't want to rush it. I wanted to take my time and try to hit the best putt I could."
Johnson, second at the Masters last week, had his fifth round in the 60s in his past six here. He stood over a birdie putt on his final hole, the ninth, when officials blew the horn and Johnson buckled his knees thinking he might have to mark his ball right there. But players had the option to finish out and secured a par.
Johnson, a South Carolina native, had not played at Harbour Town in 10 years before returning last spring. He's found the narrow fairways and smallish greens more and more to his liking. His formula for the weekend?
"Just keep doing exactly what I've been doing," he said. "I'm swinging well, placing the ball where I want to. Hopefully, I can roll in a few putts over the weekend."
Grillo, of Argentina, might not have to worry much about putting with a few more shots like he had on the 534-yard fifth hole.
He knocked his drive 282 yards in perfect position, then landed a hybrid club into the cup from 254 yards away for only the second albatross at Harbour Town since 1983 and first since 2007.
"It was a perfect shot," Grillo said. "Perfect distance. Perfect everything. Perfect wind. It was one of those that was good, but you never expect it go in."
Grillo closed his round perfectly, too, with a hole-out from 37 yards away on the tricky ninth hole.
C.T. Pan had the best round of the day at 65 and was tied with Rory Sabbatini at 6 under. Sabbatini shot a 69.
Ian Poulter led a group of 11 players who were four behind Lowry at 5 under. Poulter was among the lucky early finishers with a 67, carding six birdies during an 11-hole stretch.
Poulter held a one-shot lead after 54 holes at this tournament a year ago before ballooning to a 75 on Sunday to fall from contention.
"I've had some decent rounds around this place," he said. "I haven't really finished the week off properly yet."
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