The innovative format was played over 90 holes, with 36 holes of stroke play on Thursday and Friday cutting the field from 144 to 64, followed by six rounds of nine-hole knockout stroke play to determine a winner.
Spaniard Otaegui and Frenchman Hebert both finished three shots off the lead at five under after two days and battled through the next five matches, with huge crowds lining the fairways as host Thomas Pieters brought the European Tour back to Belgium for the first time in 18 years.
Hebert edged ahead first in the final but Otaegui hit the front on the sixth as a hat-trick of birdies guided him to three under and a second win in head-to-head competition.
Scotland’s David Drysdale finished third after beating Englishman James Heath by one shot in the 3rd/4th play-off.
Otaegui arrived in Antwerp as one the form players on Tour and secured a sixth consecutive top-20 finish on Saturday afternoon before going on to follow up last season’s maiden victory at the Saltire Energy Paul Lawrie Match Play.
“I’m very happy, very relaxed now after the last nine holes against Ben that were very tight,” he said. “I think we both played very good golf and I’m just very proud about my week.
“I just tried to play against myself. Obviously your opponent is just next to you but I just tried to focus on my game, stroke play, and so that’s what I tried to do.
“I’ve started pretty well for the moment. I’m just looking forward to focus on the Rolex Series next, some big events coming up and I just want to focus on that and there’s still a lot of season ahead. The season is still very long but I’m looking for Ryder Cup.”
Both players went right off the tee on the first to surrender bogeys but Hebert bounced back on the second, rolling in a left-to-righter from 15 feet for a birdie and the lead.
There was then a pair of pars on the third before Otaegui narrowly missed finding the water on the fourth, taking advantage of his good fortune by putting his approach to tap-in range to level the contest.
Two more pars were to follow on the fifth but Otaegui rolled in a 30-footer on the sixth and he led in the final for the first time.
Both men took advantage of the driveable par four seventh but a stunning approach to the par five eighth moved Otaegui two ahead and a pair of pars followed on the last.
Hebert is still seeking his maiden triumph after claiming six wins on the Challenge Tour.
“Adrian is a very good player, especially in this kind of format,” he said. “He’s already won one tournament in match play last year but I did my best.
“I was a bit tired for the final but there is a lot of positive things to learn about this week and that’s good.
“This format is very fun, it puts you under pressure almost every hole because everything can happen. I think it’s a great idea.”
Heath took the early initiative in the play-off with a birdie on the second but Drysdale hit back on the third. Both men made a mess of the fifth but Drysdale dropped one shot to Heath’s two and that would prove crucial.
The contest was level with a Heath birdie on the next but Drysdale made a gain on the seventh and the duo parred their way home.