Bernd Wiesberger shot a 6-under 65 on Saturday to grab the lead after three rounds of the Portugal Masters.
Wiesberger, who entered Saturday tied for second place, recorded six birdies at the Oceanico Victoria Golf Course to move one stroke ahead of Fisher at 13-under 200.
"I had to grind out the first few holes, but I kept pushing," said Wiesberger, who will seek his third European Tour win of the season on Sunday.
Fisher carded a 2-under 69 while dealing with a sprained left ankle which he suffered on the first tee Friday. The Englishman tallied five birdies and three bogeys, including one on the last which allowed Wiesberger to go in front.
"(The ankle) got heavily bandaged overnight and I tried to take as much weight off of it as I could yesterday and this morning," said Fisher. "I strapped up, went out there and played golf and a 69 is something I can feel pretty pleased about."
Richard Finch finished with a bogey-free 66 to move into a tie for third at 9- under with Michael Campbell and Shane Lowry, who both shot 67.
Mark Foster and Miguel Angel Jimenez share sixth at 8-under, while Andrew Dodt, Gonzalo Fernandez-Castano, Christian Nilsson and Fredrik Andersson Hed are knotted at 7-under -- good for eighth place.
Stephen Gallacher entered Saturday locked with Wiesberger at second place, but shot 72 in a round which was marred by a pair of bogeys and a double-bogey on the par-4 14th. The Scot is tied for 12th at 6-under.
Francesco Molinari, the only member of the victorious Ryder Cup team to make the cut, fired a 66 on Saturday to move to 5-under. Jose Maria Olazabal and Martin Kaymer were also in the field, but they failed to qualify.
Defending champion Tom Lewis, who captured his first and only European Tour victory at this event last year, carded a 70. He resides in a large group tied for 44th at 1-under.
Paired with the second-round leader, Wiesberger applied pressure with a run of six birdies in seven holes, which halted when he parred the 15th.
Tied entering the last, Wiesberger recorded another par, then watched as Fisher rimmed a 5-foot par putt.
"Obviously, I'm disappointed to drop a shot on the last," said Fisher. "It would have been nice to go out there tied with Bernd, but it wasn't meant to be. He played great."
NOTES: Wiesberger won the Ballantine's Championship and the Lyoness Open this season for his first two career wins on the tour...Dodt's 64 was the low round of the day...This is the final tournament to be played in Europe for 2012. The next time the tour will play on European soil is April, 2013.