Goosen, who also titled last week at the China Masters and five weeks ago at The International, bogeyed the 18th with two players waiting on the final tee at minus-19.
But it didn't matter.
The final pairing of Nick Dougherty and Henrik Stenson both managed only par at the last to finish with matching 68s at Golf Club Gut Larchenhof. They shared second place with David Lynn (67) and Jose Maria Olazabal (66) at 19-under-par 269.
'I have come to Germany so many years now and not done any good,' said the 36-year-old Goosen, who won despite hitting just five fairways in the round. 'To finally win one here is great.
'I have never done well in the past around this golf course either, but this week the weather was great and my putter got hot and I holed a lot of putts.'
David Howell (66) finished alone in sixth place one stroke further back, while Paul Casey (66) and Anthony Wall (70) shared seventh at minus-17.
Goosen entered the round tied for the lead with Stenson, Dougherty and Wall at 15 under. He stumbled early with a double bogey at the par-4 second, but rebounded with four birdies on the front nine. His 18-foot birdie putt at No. 7 put him into a share of the lead with Lynn and Wall at minus-17.
Wall moved to the top of the leaderboard briefly at 18 under with three straight birdies from the fifth, but Goosen joined his playing partner there with a birdie at 10 and then took the outright lead with another birdie at the 12th.
Goosen made it two in a row with a birdie at No. 13, which he played at four- under for the tournament, before moving to 21 under with a birdie at the par-5 15th.
After two straight pars, the two-time U.S. Open champion had a disastrous 18th hole, where he drove a 3-wood into the water left of the fairway.
'The breeze was a little bit off the right, but not too much, and I just felt like hitting a solid 3-wood down the left side,' said Goosen, who played the final two holes at 2 over par for the tournament. 'As soon as I saw it flying through the air I knew it was in the water.'
Goosen then knocked a 9-iron within 5 feet to set up a par putt, which he missed.
'There was a slight chance that I could have played it, but where I had to drop it the rough wasn't very thick and I knew I could get on to the green in three shots,' said Goosen.
Angel Cabrera finished alone in ninth place at 16 under after a final-round 67. Kenneth Ferrie (67) and Ricardo Gonzalez (64) shared 10th place one stroke further back.
Gonzalez's 64 was the best score of the day by two strokes. He teed off in one of the middle pairings, showing those at the top of the overnight leaderboard that low scores were possible in the muggy and foggy conditions.