Lowry, who opened with a 65, will return at 7:45 a.m. local time (1145 GMT) on Saturday to play the remaining two holes before beginning his third round.
Dustin Johnson and Argentine Emiliano Grillo shot matching 67s to finish on seven-under 135 before rain and high winds forced a suspension for nearly four hours.
Lowry collected birdies on his first two holes before the storms hit. He returned for two more birdies and a bogey.
Grillo had the highlight of the round after holing out from 254 yards for a two at the par-five fifth hole. It was the first albatross at the Hilton Head, South Carolina course since 2007 and the fourth of the year on the PGA Tour.
"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 to go in."
The Argentine also had three birdies after starting the round with two bogeys.
Johnson claimed five birdies against a single bogey.
"It was difficult all day," the world number one said. "The wind blew consistently all day. Made it tough. But I hit a lot of really solid golf shots.
"At times it was really difficult to judge the wind but I felt like I played really solid all day, gave myself a lot of opportunities."
Johnson liked his weekend chances but hoped he could roll in a few more putts.
"The greens are tricky," he said. "For me, I don't know, I've always struggled reading them. But I hit some really nice putts and I played really solid."
Xander Schauffele, who had tied for second at the Masters, shot a 70 to sit eight strokes off the lead.
Italy's Francesco Molinari, who took a two-shot lead into the final round at Augusta National before being overtaken by Tiger Woods, was unlikely to make the projected cut of even par.
Molinari was at three-over with six holes to play in the second round.
(Reporting by Gene Cherry in Salvo, North Carolina, editing by Peter Rutherford)
