Just as it looked like the Rugby Park side might emerge with a share of the spoils after frustrating a dominant Hibs, Gavin Skelton was penalised for felling the Moroccan inside the area eight minutes from time.
Following a hard-fought first half, Hibs took complete control after the interval but passed up a handful of chances before Benjelloun notched the winner.
Kilmarnock came close to breaking the deadlock as early as the fourth minute when Skelton's corner caused the hosts all sorts of problems. The set-piece was flicked towards skipper Kevin Kyle who saw his header hit the post.
Connor Sammon pounced on the follow-up but saw his attempt to place the ball into the net at the near post thwarted by Kevin McBride.
An organised Kilmarnock side were doing well to stifle Hibs although they were relieved to see a long-range Derek Riordan shot sail over the bar.
The visitors created another chance just a minute later when Jamie Hamill's cross from the right caused panic as the lively Kyle was unable to make contact inside the the six-yard box.
At the other end, Merouane Zemmama's cross proved awkward as it bobbled about in the six-yard box but Kilmarnock goalkeeper Mark Brown cleared-up.
Riordan was showing the kind of form that earned him a Scotland recall as he did well to create room for a shot 18 yards from goal, but his left-footed effort hit the side-netting.
Moments later, Anthony Stokes latched onto a long ball but his attempted chip over Brown was easily grabbed by the keeper.
The players were finally able to regain their breath during a brief lull in proceedings that saw neither goalkeeper called into action.
Hamill then went close with a curling effort from an angle in the 36th minute after showing great close control to leave David Weatherston in his wake.
Moments later Abdessalam Benjelloun unsuccessfully made an attempt to pounce on Stokes' knock down in the box just yards from goal.
Zemmama was causing all sorts of problems with his direct running and the Moroccan flashed a shot wide before the interval.
Hibs made a lively start to the second period and should have capitalised when David Wotherspoon was afforded space in the box.
Riordan's floated delivery was met by the right-back, who timed
his run into the area to perfection, but his header back across goal missed the target in the 48th minute.
Kilmarnock could not even get out of their own half, such was Hibs' dominance early in the second half with Liam Miller pulling the strings in the middle.
Zemmama then hit a left-footed shot goalwards that deflected off Sammon's outstretched leg before being picked up by Brown.
Kilmarnock weathered the storm and were able to regroup as the intensity of Hibs' pressure waned.
Frazer Wright was called upon to cut out Benjelloun's pass into the six-yard box with Stokes ready to pull the trigger.
It was all hands on deck for Kilmarnock as they battled to keep Hibs out. Zemmama turned and twisted in the box before firing a deflected shot over.
From Riordan's corner, the whistle had gone for a foul on goalkeeper Brown before Benjelloun nodded the ball into the net.
Becoming understandably frustrated by his side's failure to score despite their dominance, Hibs manager John Hughes introduced Colin Nish for Stokes.
The next chance for the home side well to Riordan as he slid in to connect with a cross but failed to keep his effort down.
Riordan was then denied by a superb low block by Brown from 15 yards after Zemmama's pass into the box was headed straight to the striker.
The former Celtic player's next attempt in the 78th minute was just too high as he attempted to find the far corner of Brown's goal.
Hibs were then awarded a penalty after Skelton carelessly bundled Benjelloun over inside the box with just eight minutes left.
The Moroccan took his time before sweeping the ball past Brown from 12 yards to seal the points.