Bradley Dredge, who won the Madeira Island Open last month, shot a 4-under 68 to finish alongside Jamie Donaldson and Brian Davis in a tie for second at 4-under-par 284.
Jacobson, who made his first start since injuring his wrist at the Caltex Masters, was part of a five-way tie for first with only a few holes remaining. The Swede jumped ahead of the pack at the par-5 17th with a chip-in eagle to climb to 6-under and open a two-shot lead with one hole to play.
At the last, Jacobson could not get up and down to save par but the title had already been secured. He tapped in for bogey and the win as playing partner Davis could do no better than par at the very same hole.
'I struggled a bit on the greens today and I think that cost me the chance of the tournament,' said Davis. 'But I made a couple of swing changes before this week so to finish second is pretty good and I was pleased the way I hung in there when the going got tough.'
Jacobson started the day with a slim lead over Davis and chipped in for birdie on the first hole at Vale do Lobo to jump out of the gate. The difficult layout and blowing winds caught up with Jacobson, however, resulting in three bogeys over the next five holes for the 28-year-old.
He recovered at the seventh and knocked his second shot to 12 feet for a birdie. Around the turn, Jacobson failed to save par from seven feet for a bogey at the 12th.
Again, Jacobson responded. He birdied the 15th to move back into a share of the lead before the remarkable eagle at the 17th.
Jacobson left his second shot short of the green at the par-5 and chipped his third into the cup.
With the victory, Jacobson joined Ernie Els as the only two-time winners on the European Tour this season. Jacobson won his first at the Hong Kong Open, the second event of the 2003 campaign.
Greg Owen, who held a three-shot lead after 36 holes, posted a 73 to finish alone in fifth at 3-under-par 285. James Kingston was two shots further back at 1-under-par 287.
Jarmo Sandelin carded a 68 to finish at 1-over-par 289. He was joined by David Lynn, Carlos Rodiles and Marcel Siem in a tie for eighth.
England's Richard Walker was the low amateur in the field. Walker shot a final-round 71 to finish in a group at 3-over-par 291.