Jacobson, who earned his first victory on the European Tour early this season at the Hong Kong Open, is making his first start since injuring his wrist at the Caltex Masters. The 28-year-old got things going with three consecutive birdies starting at the third and collected back-to-back birdies from the seventh to go out in 32.
'I went to see a doctor in Sweden but they couldn't find anything serious on the X-rays, it is probably just a little bit of inflammation,' said Jacobson. 'It is still there a little bit now but I can't rest any longer.
He shared the lead with Owen throughout the back nine and took sole possession of first with a birdie at the 15th. Owen matched him at 6-under with a birdie at the par-5 17th but Jacobson drained a 12-foot putt at the very same hole to regain the outright lead.
Jacobson then added a birdie at the last to shatter the course record by two strokes.
'I felt very comfortable once I had got started and made a few birdies,' said Jacobson. 'It is fair to say that I am amazed to have shot 64 because it has been such a long break and I am normally a bit of a slow starter. But it is nice to get a good round in.'
Owen also faired well in the afternoon. The Englishman torched the front nine with a stretch of four consecutive birdies starting at the par-4 second and added a birdie at the eight to make the turn at 5-under.
The 31-year-old stumbled with a bogey at the 14th but recovered with two birdies down the stretch to finish alone in second.
'It is nice to see yourself peppering the flag and that is what I'm working on with my brain trainer, just try and visualize what you do on your home course when you are out playing tournaments,' said Owen. 'It is the same game after all, just a different location.'
Bradley Dredge, who captured the Madeira Island Open last month, was joined by Carlos Rodiles in a tie for third at 3-under-par 69.
Graeme McDowell, Gustavo Rojas, Euan Little, Brian Davis and Van Phillips, who won this event in a playoff in 1999, were one shot further back at 2-under- par 70.
Anders Hansen, Klas Eriksson, Philip Walton, Mark Roe, Andrew Coltart, Marcel Siem, Lee S. James and David Lynn finished tied for 10th at 1-under-par 71.
A total of 17 players were under par at the difficult Vale do Lobo layout and the majority of the players in the field found themselves on the other end of the draw.
Two-time champion Phillip Price carded a 1-over 73 while fellow Ryder Cup member Lee Westwood's struggles continued with a dismal 81.