The 28-year-old Jacobson shot a course record 64 in Thursday's opening round. His round on Saturday left him at 5-under 211, one stroke ahead of Englishmen Brian Davis and Greg Owen.
"I just wanted to try and dig in today and stay close enough to have a chance (Sunday), so obviously I'm delighted to find myself in the lead," said the Swede, who was one of just four golfers to break par Saturday in the tough conditions.
Jacobson had three birdies and a bogey on the front nine and had a bogey 5 at the 12th hole when he overshot the green. Jacobson had nothing but pars the rest of the way and put himself into position for his second win of the season. His previous win was at the Omega Hong Kong Open.
"I wasn't surprised because it was the toughest conditions of the week," said Jacobson, who shot a 76 on Friday. "I was happy to start off that way and it gave me a bit of confidence to get in the round properly."
Owen entered Saturday with a three-stroke lead, and had eight pars and a birdie on the front nine. But things then fell apart as Owen gave away five shots on the back nine, including a double-bogey 6 on the 14th, and stumbled to a 76.
Davis held his ground with a second straight round of 71, posting a birdie on 13 before finishing with five straight pars.