Choi had a stellar round of his own with a 9-under 63, but Jacobson made Golf Club Gut Larchenhof his own.
'I think today was just about the perfect round of golf for me,' said Jacobson, who also set a career best with the 18-hole score. 'I don't think I could really ask for anything more. You can't make every putt in the round but I made more than my fair share.'
Jacobson played the back side first and jumped out of the gate with a birdie at the 10th. He then ran off three consecutive birdies starting at the par-4 12th before picking up another birdie at the 17th.
At the par-4 18th, Jacobson hit a brilliant approach that rested within two feet of the cup. He tapped in for birdie to make the turn at minus-6 in preparation to torch the front nine.
Jacobson hit it close again at the par-4 second and rolled in a three-footer for birdie. He sent his second shot to the par-5 third to 10 feet for an eagle and followed that up with a birdie at the par-3 seventh to reach 10 under after 13 holes.
The Swede parred his next two holes before converting an eight-foot putt for a birdie at the par-5 seventh. Jacobson then knocked his tee shot to 10 feet at the par-3 eighth and ran home the putt to move to minus-12.
Jacobson needed to birdie the ninth to become the first person to ever break 60 on the European Tour but the 28-year-old found trouble off the tee at the par-4.
His drive plugged into the thick rough and Jacobson's second shot missed the putting surface. Jacobson chipped his third past the cup and converted a difficult putt coming back to save par.
'If you haven't had any errors earlier in the day, it would have been a shame to finish with a bogey,' said Jacobson. 'So it was great to hole that putt and great to move alongside all the other great players on the European Tour who have shot 60.'
Jacobson certainly has entrenched his name in the record books alongside several prominent names who have shot the mark including European Ryder Cup captain Bernhard Langer, who fired a 60 at this event in 1997 en route to his third of four German Masters titles.
'To shoot 60 is fantastic because I haven't really been close before,' said Jacobson, who has won twice on the European Tour in 2003. 'It was just one of those days when you start off playing well and just keep it going.'
Choi, looking to fine tune his game for his Presidents Cup debut later this year, also started on No. 10 and collected five birdies over his first six holes.
The 33-year-old drained a three-foot putt for a birdie at the third and followed that up with a birdie at the fourth.
Choi added two birdies over his last four holes to finish alone in second.
Darren Clarke collected five birdies and an eagle for a round of 65. He was joined by Paul Casey, Gary Orr, Ian Poulter and Carlos Rodiles in a tie for third.
'I could have been 4 or 5 under after the first five holes but I wasn't, which was a little disappointing,' said Clarke, who won the WGC-NEC Invitational in August. 'But I didn't push it, didn't try to force anything.'
Adam Scott, Marcus Fraser, David Gilford, David Howell, Brett Rumford and Steve Webster share eighth place at 6-under-par 66.