Gibson, Minnesota's No. 16 prospect, held the Desert Dogs to four hits in the win, throwing 53 of his 72 pitches for strikes in his first outing since making a pair of late starts for Triple-A Rochester.
The right-hander appeared in 13 games this season in his comeback from Tommy John elbow surgery last year but did not toss more than four innings in any official contest.
"It feels good to pitch into the fifth for sure," Gibson said. "I did it a couple of times in the Instructional League, but to do it in the Fall League against the quality of guys here makes it better. I did get tired as it went along, but it didn't happen until the fifth. When I was at Triple-A, it hit me in the fourth. So that's a positive."
The 25-year-old induced an inning-ending double play from A's prospect Grant Green to erase a single in the first and struck out two in the second to pitch around a pair of singles.
The 6-foot-6 Gibson worked a 1-2-3 third, struck out two more in a perfect fourth and fanned two more in the fifth to end his first outing of the fall.
Although he admitted that certain innings could have gone smoother, the University of Missouri product believed Thursday's outing was a good building block.
"I've got a couple of goals while I'm here," he said. "The first is stay healthy, obviously. Then, there are some mechanical things that need work, like working out of the stretch and making sure I'm coming down correctly. Finally, it's just going out there, competing and giving my team a chance to win.
"Taking 10 months away from the game, they say you lose some of that hunger to compete. I want to make sure I'm not just satisfied with being healthy but also putting out quality starts as well."
Peoria scored a pair of runs in the third on a throwing error by Phoenix catcher Jake Realmuto (Marlins). An inning later, Reds slugger Donald Lutz hit a triple, one of his three hits, and scored on an error by Rays top prospect and Dogs shortstop Hak-Ju Lee.
Marlins southpaw Brian Flynn, a 6-foot-8 Wichita State product, allowed two runs on five hits over three innings in his first start for Phoenix. He struck out one and threw 23 of his 28 pitches for strikes.
Danny Wild is an editor for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.