Wagner shot 3-under-par 69 on Friday to take the outright lead in the Houston Open before an afternoon storm delayed play for an hour and 45 minutes. More rain came later and the second round was suspended at 7:25 p.m. with 36 players still on the course.
Wagner was in at 12 under, three ahead of Charley Hoffman (70) and Mathew Goggin, who shot 64. Chad Campbell was 7 under after matching Goggin's 64.
Defending champion Adam Scott, who shared the first-round lead with Wagner after they set the course record with 9-under 63s, had five bogeys and a double in shooting 76.
Play was halted just before 2 p.m. The round resumed at 3:34 p.m., with the course softened, but the temperature more than 20 degrees cooler.
Phil Mickelson beat the bad weather and shot 68, but he was eight behind the leader, who is looking for his first victory in 45 career starts.
The 28-year-old Wagner admits he'll have to control his emotions over the weekend as he tries to win a trip to the Masters.
"You have to use it to your advantage," Wagner said. "Nerves don't have to be a bad thing. They can always be a good thing."
He stayed in a house off the first hole at Augusta in 2004 and played 36 holes two consecutive days. During one round, his approach to the par-5 15th plugged in the side of the bank.
His great uncle promised that would never happen during the Masters. Wagner is determined to find out for himself.
"I definitely know I'm going to be there some time, whether it's next week or five years from now," he said. "I look forward to playing there in the tournament."
Wagner was in the second group to tee off Friday morning and he moved to 12 under on his opening nine. He got up and down from a greenside bunker on the par-5 fourth, sank a 6-footer for birdie on the 5th and added another birdie on the par-5 eighth, the third-easiest hole during the first round.
He sliced his drive into the water on the par-4 11th and bogeyed, then got the stroke back with a birdie on 13.
Davis Love III, needing a win to qualify for the Masters, was 3 under after two rounds. Love has started 70 consecutive major championships, the longest active streak.
John Daly played seven holes, then withdrew because of a back injury.