The former Ryder Cup star claimed four birdies on the front nine and another three on the back, but could only manage a five at the par-four 18th on the PGA West Stadium Course in La Quinta in California.
That meant South Korea's Dong-hwan Lee took the Qualifying School leader's medal by a stroke on 25 under overall after six rounds, while America's Steve LeBrun finished alongside Fisher on 24 under.
Richard H Lee, Billy Horschel and Kris Blanks finished tied for fourth.
Overnight leader Steven Bowditch could only manage a two-over 74 but, on 21 under, finished easily inside the top 25 and ties, who qualified for next year's Tour.
Among them were Si Woo Kim, who at 17 years and five months became the youngest player to earn a card through qualifying school as his four-under round saw him finish in a share of 20th on 18 under.
He will not be able to take his place on Tour, however, as he does not turn 18 until June.
There was agony for America's Edward Loar, who was tied for third overnight but, after a six-over 78 which contained two double bogeys, fell to joint 32nd.
Among those to miss out were England's Oliver Fisher, New Zealand's Danny Lee and Camilo Villegas of Colombia, as well as Americans Heath Slocum and Billy Mayfair.