Brought in by Martin Jol after being marginalised at Aston Villa, the loan signing came off the bench to secure a 1-0 win and potentially the Dutchman's position at the helm.
It was not a comfortable victory for Fulham, far from it, but it was their first since the opening day of the season and first at Craven Cottage since April 1.
It had looked like their miserable run would continue as Stoke dominated the first half of Mark Hughes' first return to the ground since leaving citing a lack of ambition in the summer of 2011.
Stoke were denied a clear-cut penalty when Philippe Senderos took down Stephen Ireland and Fernando Amorebieta was fortunate not to concede a spot-kick soon after for a challenge on Jonathan Walters, which was adjudged to be outside the box.
Robert Huth also had a header cleared off the line by Sascha Riether in a first half they controlled, although Fulham were denied a penalty when Bryan Ruiz was felled by Marc Wilson in stoppage time.
The tension was palpable and Craven Cottage exploded when Bent slotted home seven minutes from time, securing victory in a match Jol admitted in his programme notes was a "huge game for us all".
The hosts attempted to set the early tempo, although their lack of confidence was evident as several passes went awry in the opening 10 minutes.
Pajtim Kasami, shifted to the right to accommodate Ruiz as the number 10, was fortunate not to receive early punishment after flinging an arm out in the direction of Erik Pieters.
The Stoke left-back made a meal of the contact but Kasami was fortunate not to see his petulance punished by referee Roger East.
Marko Arnautovic fired the first chance of the match wide and Stoke should have been awarded a penalty in the 16th minute.
Ireland burst down the left flank and looked as though he was brought down at the byline by Senderos, only for referee East to award a goal kick.
The Stoke pressure continued and they had another penalty shout turned away soon after. Amorebieta was booked for clumsily bringing down Walters, but the linesman adjudged the foul to have taken place on the edge of the box.
Things were just not falling for City, with a Huth header from a Matthew Etherington corner set for the top corner until Riether cleared off the line.
Steve Sidwell and Amorebieta flashed over wildly as Fulham regained composure, with the former then seeing a header clip the crossbar before Ruiz was denied a penalty in first-half stoppage time.
The Costa Rica international was clipped in the box by Wilson, but East waved play on to the anger of home fans.
Huth headed over shortly after the restart, although Fulham were looking a more threatening attacking unit.
Begovic just beat Dimitar Berbatov to a low Riether cross as Fulham pushed for an opener, although the offside flag would have cancelled it out had he managed to prod home.
The Bulgarian, scythed down by Glenn Whelan minutes earlier, was limping and soon had to be replaced by Bent.
At the other end, Arnautovic broke clear and lobbed the ball over Fulham goalkeeper David Stockdale, although the whistle had already gone for offside - a harsh decision.
Ireland flashed a left-footed volley just wide as Stoke continued in the ascendancy and Huth again had a header cleared off the line by Riether as the match entered the final 10 minutes.
Just when it looked like another afternoon of frustration for Fulham, up popped Bent to save the day.
Collecting a deflected Kasami shot, he turned away from Huth and Begovic in the box to slot home, with Craven Cottage exploding with emotion.
Stoke pushed for a leveller but Fulham held out for just their second clean sheet in 18 home matches, ending their run of conceding costly late goals.