The Englishman entered the final day at Doha Golf Club level with his compatriot at the top of the leaderboard and while he opened up a three-shot lead at the turn, an impressive fightback by Fisher meant the pair were separated by a just single stroke as they went up the par five last.
It was advantage Fisher after two shots with Pepperell in the rough after both men laid-up but the 27 year old hit an excellent third to set up a par which his playing partner could only match.
Pepperell’s closing round of 70 got him to 18 under, with Fisher signing for a 71 and Swede Marcus Kinhult finishing at 16 under after a 68.
Spanish duo Gonzalo Fernandez-Castaño and Pablo Larrazábal, Frenchman Grégory Havret and Italian Renato Paratore were then at 15 under.
Pepperell won the ALLIANZ Open Côtes d’Armor Bretagne en route to graduating from the Challenge Tour in 2012 and then enjoyed three consistent seasons but lost his card in 2016, leading to a successful trip to the Qualifying School.
His bounceback season was a triumph, securing four top fives and three top tens from his last ten events in 2017 and he now has a European Tour victory in his 129th event.
Pepperell started his round with eight straight pars and that was good enough to hand him a three-shot lead as Fisher made a hat-trick of bogeys from the fourth.
This will give me confidence. When you win, you know you can win. I’ve always felt and believed I will win out here – Eddie Pepperell
The bad run started with a three-putt from 20 feet before he hit a poor tee-shot on the fifth and failed to get on in regulation, and then failed to find the green again with his second on the next.
Paratore was the man to cut the lead to two as he charged through the field, making a hat-trick of birdies from the tenth after turning in 35 to sit three off the lead before rolling a slippery one down the hill on the 14th.
Fernandez-Castaño had also turned in 35 and he took advantage of the par five tenth before chipping in from a tricky lie at the 11th to join Paratore, but they were soon three back as Pepperell broke his run of pars with a textbook birdie after laying up on the par five ninth.
The gap was back at two after a long Fernandez-Castaño putt on the 12th but Pepperell made another picture-perfect birdie on the tenth before Paratore birdied the last to set the target at 15 under.
Pepperell made an early contender for bogey of the season on the 12th on Saturday when he chipped in after hitting the rocks three times and he made another five in round four, although this time he hit the rocks once with his second and failed to get up and down.
The group at 15 under then started to swell, as Fisher made birdies on the tenth and 12th before dropping a shot after a plugged lie on the next but regaining it on the 14th.
Larrazábal made a birdie on the first and had been just two back after an eagle on the tenth. He bogeyed the 15th but then made back-to-back birdies on the 16th and 17th.
Kinhult turned in level par but he picked up shots on the tenth, 13th and 16th and the group in second was now a pack of five.
That was just two shots back when Pepperell hit a poor tee-shot on the 15th and had to lay-up on the par four, with Fernandez-Castaño and Larrazábal both parring the last to finish at 15 under.
An excellent tee-shot on the 17th helped move Havret to that mark after he had turned in 36 but made gains on the tenth and 14th, and he stayed there after a closing par, with playing partner Kinhult making a birdie to set the target at 16 under.
Pepperell spun an an excellent approach into the 16th to bring a birdie and a fist-pumping celebration but Fisher followed him in after a nice approach of his own and a tee-shot to tap-in range on the next meant the gap was one heading up the last.
South African George Coetzee and German Sebastian Heisele finished at 14 under, a shot clear of England’s Matthew Baldwin, Frenchman Mike Lorenzo-Vera and Spain’s Adrian Otaegui.