Thomas played six holes in the morning, nearly holing a 9-iron and then making par with a flop shot on the green and over the bunker on the par-3 sixth as he completed a 6-under 65 to share the 36-hole lead with Scott, who also had a 65.
They started the third round in the afternoon with only about 45 minutes of daylight, and Thomas holed a 12-foot eagle putt to take the lead. Scott missed his eagle attempt on the par-5 opening hole.
The final group hit tee shots on the third hole when it was too dark to continue. They were to resume at 6:45 a.m. to complete the third round, and then the 76 players who make the cut will head right back onto the course in the same groups to try to finish.
Thomas was at 13-under par through two holes of the third round.
"There's so much golf to play," Scott said. "It feels like it's late in the tourney, but it's only halfway."
Tiger Woods completed seven holes and they were impressive, but he remained seven shots behind, and he stopped playing after his third shot on the par-5 17th came up short of the green.
Patrick Rodgers, who completed a 67, opened with an eagle and was two shots behind Thomas.
The start of the tournament was delayed seven hours by rain Thursday and has been trying to catch up, creating a disjointed feel to the week. Thomas said he could barely feel his toes when he warmed up Saturday morning in temperatures in the low 40s and darkness as he set out to finish the second round. He also was up before dawn on Friday to get ready to start his opening round.
Imagine how he felt when told when the third round was to resume.
"I'm still trying to get over that 6:45 a.m. start I just heard," he said. "That's in a couple of hours."
Conditions were so good that players wanted to get in as many holes as they could, so they launched tee shots on No. 3. But darkness sets in quickly off Sunset Boulevard, and they had no choice but to stop. Scott could hardly see the flag from 136 yards away.
"I have no depth perception because I can't see the flag," Scott said.
Michael Thompson, who didn't get into the tournament as the first alternate until Sunday, was at 10 under.
Rory McIlroy finished off a 63 in the morning to get back in the game, and he had one birdie through three holes in the third round. He was playing with Jordan Spieth, who had a 70 in the morning to finish four behind. Spieth three-putted for par on the opening hole, missing from 3 feet, and three-putted from the fringe on No. 3 for a bogey to fall six shots behind. He also missed a 10-foot birdie on his final shot of the day.
But there is a long way to go. Saturday night usually feels like the end is near. Instead, the final group still has just under half the tournament to go. Woods, while seven shots behind, still had 29 holes to play.
Information from The Associated Press was used in this report.