The 45-year-old began the fourth round three shots behind overnight leader Elvira but went in front courtesy of five birdies on the front nine and remained ahead by one stroke as the final group arrived at the 18th tee.
But there was late drama as the heavens opened, with a clap of thunder on Elvira's backswing disrupting his approach into the 18th green just before play was suspended at 1450 local time.
That left the Spaniard with a 30 foot putt to keep his hopes alive and when play resumed at 1630, he coolly drained his birdie effort to join Hend on 15 under par and force a play-off.
Hend got a lucky break when his tee shot at the first extra hole hit the base of a tree and landed on the fairway, while Elvira's ball went straight into a fairway bunker.
The Australian hit another tree with his second shot but holed his birdie putt from three feet to clinch the title and banish memories of previous play-off defeats at the Omega European Masters in both 2016 and 2017.
The victory is Hend's first since the 2016 True Thailand Classic Presented by Chang and takes him into the top ten of the 2019 Race to Dubai Rankings Presented by Rolex.
Elvira's runner-up finish was his second in as many starts after he ended the Commercial Bank Qatar Masters in a tie for second in his last outing.
Jazz Janewattananond was another two shots back in third after mixing five birdies with two bogeys in his closing 69.
Meanwhile, four time Major Champion Ernie Els secured his 300th career top ten finish after closing with a 71 to join the large group in a tie for seventh.
Hend started brightly on Sunday, holing his birdie putt from around four feet at the first before rolling in from a similar distance on the fourth to get within one shot of the lead.
The Australian drained two monster birdie putts at the sixth and seventh holes to join Elvira at the summit on 14 under.
And he took the outright lead when he closed his front nine with a fifth birdie of the day from eight feet.
Hend dropped a shot after getting into tree trouble on the tenth but took advantage of the long 13th for the fourth day in succession, tapping in his close range birdie putt after his eagle attempt had just evaded the hole.
Elvira reduced the gap to one shot when he rolled in his birdie putt on the 16th green before holing his pressure putt at the 18th after the weather delay to take the contest to extra holes.
Hend rode his luck in the play-off to earn a hard fought victory.
He heaped praise on Elvira after edging their final round battle.
"What a putt by Nacho," said Hend. "If I was to go out there and hit that putt you would say you would hole it one in ten times. It was an amazing putt, and in the situation he holed it. All credit to Nacho, it was fantastic.
"I had to get off to a fast start as I was three shots behind. That's all there was to it. I was fortunate enough to turn in five under and on the back nine I shot level par. I can't ask for much more on a Sunday when the golf course is playing quite tricky.
"I felt like I played fantastic on the back nine. I nearly holed a lot of putts, just missing. I just had to keep my head on and stay patient, stay in there. The worst case scenario was a play-off.
"I'm a grinder and a fighter. So is my caddie Tony. We both have the same mental attitude. It doesn't matter how old we are, we work hard at what we do. It just takes a bit of luck to win.
"Obviously I had a bit of luck on the play-off hole. If you don't have any luck you won't win. I had the luck today, unfortunately for Nacho. His time will come, he's going to win. He's a great player."
Elvira was pleased with his performance despite just missing out on a first European Tour title.
He said: "It was thunder in a bad moment but the gods did give me one back with that putt. I think I played great all week, solid, consistent, I'm very happy with that. I'm happy that my game has finally showed a little bit of consistency.
"I tried to give it all on the play-off hole. I just missed my driver a little bit and gave myself a little chance to make birdie, but I'm happy.
"Lifting trophies is the point, that's what we try to do every week. Hopefully it works out soon."