Isao Aoki and Allen Doyle each shot rounds of 5-under 67 to finish tied for third at 8-under-par 136.
Rain delayed the start of the second round before the players finally took to the TPC at Jasna Polana at 1:30 p.m. EDT under cold and dreary conditions.
Thorpe and Jacobs were tied atop the leaderboard after both players shot opening rounds of 7-under 65. Thorpe quickly broke the tie with a 15-foot birdie at the first.
Jacobs soon joined Thorpe after he knocked his approach within six feet for birdie at the fourth only to fall back into second with a bogey at the following hole. However, two holes later Jacobs made another birdie and the duo was again knotted atop the leaderboard.
'I played okay,' said Jacobs. 'Kept hitting it fat all day.'
Jacobs took the outright lead at the 10th after he knocked his approach within seven feet to move to 9-under. The lead was short-lived as Thorpe made a birdie of his own at the very next hole.
At the 13th, Thorpe rolled in a 20-foot putt to save par and took the solo lead as Jacobs two-putted for bogey from a shorter distance.
Jacobs regained a share of the lead with a five-foot birdie at the last but Thorpe was intent on going into the final round alone in first.
Thorpe recovered from a bad drive at the par-5 18th after he hit his third shot within five feet of the hole. He drained the birdie putt to grab the top spot.
'First of all it was a long day,' said Thorpe, who is looking for his second win of the year. 'I hit some good shots but couldn't get any putts going. We'll go out tomorrow and have some fun.'
Both players met in a playoff to decide the Senior Tour's first major championship of the season at The Tradition last month. Thorpe got the best of Jacobs with a birdie on the first extra hole for his first major title.
Hale Irwin had four birdies on the front nine to pull within one of the lead Saturday before running into trouble on the back side.
Irwin made double-bogey at the 10th but recovered with birdies at 12 and 15 for a round of 68. He was joined by Mike Hill three shots off the lead at 7-under-par 137.
Full-field scores from The Instinet Classic