'I just wanted to try and dig in today and to stay close enough to have a chance tomorrow, so obviously I'm delighted to find myself in the lead,' said Jacobson.
Jacobson was alone atop the leaderboard after the opening round thanks to a course-record 64 but fell four shots off the pace heading into the weekend. He picked up three birdies and one bogey on the front side at Vale do Lobo to make the turn at 6-under, still three shots behind overnight leader Owen.
'I played really well on the front nine and hit every green where I had a lot of chances,' said Jacobson. 'I was happy to start off that way and it gave me a bit of confidence to get into the round properly.'
Jacobson didn't have to do much on the inward half and the Swede even dropped a shot with a bogey at the 12th but it was Owen who fell apart.
Owen started his second nine with a bogey at the 10th and nearly knocked his ball out of bounds at the 12th en route to another bogey to fall back to minus-7.
At the 14th, Owen managed to hit his ball out of bounds on his way to a double-bogey. He then dropped a shot at the 15th to fall to 4-under, one behind Jacobson.
Jacobson, who is making his first start since injuring his wrist at the Qatar Masters, parred out to take the lead into the final round. The 28-year-old is in search of his second career victory on the European Tour, having won his first at the Hong Kong Open, the second event of the 2003 season.
'As for tomorrow, I feel comfortable and I feel happy to be up there,' said Jacobson. 'First week back after 10 weeks out and now after a few more rounds under my belt I am starting to get back into it so I am very positive for tomorrow.'
Owen was in control early in his round. The 31-year-old knocked his second shot to three feet for a birdie at the fourth and made the turn at 9-under par. However, Owen's day turned into a disaster on the back half as conditions became more difficult.
He regained some of his composure over the closing holes with a difficult par save at the 17th and a two-putt par at the 18th as rain from an oncoming storm began to fall.
'I played okay but I felt like I just didn't get any breaks,' said Owen, who posted a 76 on Saturday. 'But I'm still only one shot back and hopefully that's my bad round out of the way and I can build from this.'
Richard Sterne of South Africa posted the only sub-70 round on Saturday with a 69. He was joined by Germany's Marcel Siem in a tie for fourth at 1-under- par 215.
Phillip Price, who is seeking his third title at this event, shot a 72 to finish one shot further back at even-par 216. Price was joined by Jamie Donaldson, Charl Schwartzel, Bradley Dredge and Carlos Rodiles in a tie for sixth.