The pair have not enjoyed the best of starts to the season, with six missed cuts from ten combined events, but they found their form in the Qatari capital and will head into today at 16 under, two shots clear of American Sean Crocker.
Pepperell entered the day a shot off the lead but a birdie on the first gave him a share – further gains on the fifth, seventh and tenth had him two ahead.
He chipped in for a superb bogey on the 12th after hitting the rocks in front of the green three times, but he would soon lose his lead to a sensational finish from Fisher.
The 29-year-old birdied the third, fifth, eighth and 11th and, after a bogey on the 12th, he made further gains on the 15th, 16th, 17th and last to lead by two.
Pepperell bounced back from his bogey with a gain on the 13th and he made two more on the 16th and 18th to get back into a share of top spot.
“I am looking forward to it,” Pepperell said. “Mentally I feel like I’m up for it – I wanted to lead today. I didn’t want to be behind the leader.”
Fisher added: “I gave myself some chances coming in and thankfully I made them. We’ve still got one round to go but I’ve certainly put myself in a good position. The most important thing for tomorrow is to go out and enjoy it. I’m good friends with Eddie so hopefully we’ll have a bit of fun out there.”
Crocker fired a 67 to get to 14 under, two shots clear of England’s David Horsey, Italians Lorenzo Gagli and Andrea Pavan, Frenchman Gregory Havret and Swede Marcus Kinhult.
Stephen Gallacher had only been a shot off the pace before play started yesterday but he ended the day on eight under – eight shots adrift of Fisher and Pepperell – after a poor 74 that included four bogeys.
Fellow Scot Marc Warren is also on eight under after a third-round 70, while Paul Lawrie (71 for five under), Grant Forrest (74 for two under) and Scott Jamieson (75 for one under) are further down the leaderboard.