He shared the first-round lead with Johnson Wagner after they shot course-record, 9-under 63s Thursday. But Scott, who has been ailing all week, struggled to a 76 Friday.
Wagner shot a 3-under 69 early Friday to take the outright lead at 12 under.
While Scott faltered, another Australian moved into contention. Mathew Goggin shot a 64 to move within three shots of Wagner before an afternoon storm delayed play for 1 hour, 45 minutes on Friday. More rain came later and the second round was suspended with 36 players still on the course.
Nicholas Thompson wrapped up a second-round 70 on Saturday morning to join Ben Crane and Jose Maria Olazabal at 5 under. The third round was to begin about 11 a.m. EDT and sunshine was forecast for the rest of the weekend.
Scott played 14 holes after Fridays rain and finished with five bogeys and a double bogey
Goggin picked up the slack for the boys from Down Under, kick-starting his round with two eagles on the front nine. Charley Hoffman joined Goggin at 9 under after a 70.
Six Aussies have won eight Houston Opens, including Scott last year and Stuart Appleby in 2006. Appleby was the runner-up to Scott in 2007.
Goggin joked about why Australians have had so much success in this tournament.
Maybe were just better on courses you dont have to think around, he said. You just smash it and go find it. You dumb it down for us and we do all right.
Goggin blames erratic putting for his up-and-down year'two top-20 finishes and two missed cuts in eight starts. He finished tied for 50th in New Orleans last week and came to Houston ranked 136th in putts per round (29.62).
He solved that issue on the fifth hole Friday by holing an 8-iron shot from the fairway and a bunker shot for another eagle on the par-5 eighth.
All of a sudden, I didnt hit a bad shot for the rest of the day, he said.
Goggin added birdies on Nos. 10, 12, 13 and 15 and wrapped up his round with only 25 putts.
Scott bogeyed No. 2, his first at the Tournament Course at Redstone in 56 holes dating to last years second round. He was playing the fifth hole when 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. Scott missed the green with his tee shot on the par-3 ninth, then drove into the water on the 11th to slip to 6 under. He birdied 15 and 16 before finishing bogey-double bogey.
Phil Mickelson beat the bad weather and shot a 68 on Friday, but he was eighth behind the leader, whos looking for his first victory in 45 career starts.
The 28-year-old Wagner admits hell have to control his emotions over the weekend as he tries to win a trip to next weeks Masters.
You have to use it to your advantage, Wagner said. Nerves dont have to be a bad thing. They can always be a good thing.
Wagner was in the second group to tee off Friday 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.
Wagner was born in Amarillo and that gives him an edge'Texans have won six Houston Opens. Thats also good news for Chad Campbell of Andrews, Texas. He matched Goggins 64 and sits five off the lead.
Campbell hit a 3-wood within 10 feet on the par-5 4th, then reeled off four straight birdies early on the back nine to climb up the leaderboard. Campbell has won in Houston before, beating Charles Howell III by three shots at the 2003 Tour Championship.
Anytime you can win, especially in your home state, its great, he said. Got a lot of fans, family and friends out here this week, so it would be great.