The Englishman entered the final day at Chervò Golf Club alongside countryman Laurie Canter three shots clear of the field but they were reeled in on a dramatic afternoon in Brescia.
At one point late in the day there were eight players within one shot of the lead before McGowan holed a spectacular bunker shot at the 16th to knock Canter out of the lead for the first time in over 72 hours.
Canter hit back with a birdie from six feet on the par three 17th but McGowan put his third into the par five last to 20 feet and holed the putt for a 71, a 20 under par total and a one shot victory over Canter and Belgian Nicolas Colsaerts.
German Sebastian Heisele finished at 18 under, a shot clear of countryman and two time Major Champion Martin Kaymer, Spaniard Adri Arnaus, South African Dean Burmester, Northern Ireland's Jonathan Caldwell and Norwegian Kristoffer Reitan.
The 38-year-old has not finished in the top 150 on the Race to Dubai since 2010, graduating from the Qualifying School in 2015 and 2017 but, after claiming a third European Challenge Tour win last season, he is now back to his best and back on the European Tour.
"I can't believe it," he said. "I hit the ball terrible today but luckily the putter kept me in it again.
"The tee shot on 16 was a shocker, the second shot wasn't much better and then I holed the bunker shot so I think that was the one that gave me a bit of belief. Then to roll that putt in there (on the 18th) was magical.
"I didn’t really foresee this, my form hasn’t been great. But I felt like I was playing better, definitely around the greens.
"I think I’m going to have to go now and have a nice big glass of red wine and think about what’s next."
McGowan found sand at the third and then missed a short putt to hand Canter the solo lead, with both men laying up and holing from around ten feet to birdie the par five fourth.
McGowan found water off the tee at the par three fifth for a double bogey but put his second on the par five sixth to 14 feet and rolled in an eagle to get the shots straight back.
Canter had three putted the fifth from 50 feet but a two putt birdie on the next edged him back in front before he failed to get up and down on the seventh and both players were back where they started at 19 under, although the lead was now just two.
That soon became one when McGowan got in trouble down the right and Canter three putted on the eighth, and they soon had some company.
Burmester had failed to get up and down from just off the back of the second but the big hitter made the most of the fourth and sixth and then hit a wonderful second from the rough to six feet at the tenth to move to 18 under.
Heisele had also made a slow start with a bogey at the first after a poor tee shot but he put his tee shot to ten feet at the second, took advantage of the par fives on the front nine and then holed from the fringe at the par five 11th to make it a four way tie.
Canter's 37 was the first time he had played the front nine over par all week but he recovered on the tenth with a beautiful tee shot and an approach to six feet to break out of the pack, before a two putt birdie on the next had him two ahead.
McGowan holed from 25 feet at the 13th to trim the lead to one but with both of the final group bogeying the next, Heisele and Burmester were still right in the mix despite dropping shots on the 13th and 14th respectively.
Colsaerts was also two off the lead as he recovered from a bogey after a poor tee shot at the first with a tap-in at the third, a two putt birdie at the gettable sixth, and a putt from the fringe at the 12th.
A poor chip at the 15th from Canter meant we were tied again and when Colsaerts put his second to four feet at the 16th, there were three at the top.
McGowan went a long way left off the 16th tee and after going from one bunker to another, he holed that shot from the sand to set up the big finish, with Colsaerts and Heisele both falling short despite picking up shots on the last.
Canter had held the lead since Thursday morning after a spectacular 60 but finished the week with a 72 as Colsaerts signed for a 68 and Heisele registered a 69.
Reitan carded a 65, Caldwell and Kaymer both signed for rounds of 68, Arnaus went round in 69 and Burmester finished with a 71.