Benjamin struck from the penalty spot five minutes from time to cancel out Kenny Miller's 57th minute opener for Wolves.
Miller's 23rd goal of the season had looked set to send Wolves into the play-offs on the back of an impressive win.
But Wolves, who will now face Reading in the play-off semi-finals, paid the price for failing to make the most of the chances they created.
Benjamin made them pay when central defender Ludovic Pollet was adjudged to have handled the ball.
Wolves should have been well in control inside the opening 25 minutes, but a combination of some poor finishing and the heroics of Leicester goalkeeper Ian Walker kept them at bay.
Welsh international striker Nathan Blake dragged his close-range shot wide in the 18th minute after good work by his strike partner, Miller.
Walker then frustrated Wolves with a stunning save when he dived full length to tip away a 20-yard drive from Scottish international midfielder Colin Cameron.
Miller then shot weakly at Walker from close range following good work from Cameron before Leicester threatened to make Wolves pay for the failings in front of goal.
Leicester striker Brian Deane simply waltzed around the goalkeeper Matt Murray on the edge of the Wolves area.
Deane was faced with an open goal, but his shot lacked the required pace and retreating Wolves left-back Lee Naylor was able to clear the ball off the line.
Miller proved to be more clinical when his chance arrived, but the strike owed everything to the pace and power of the former Rangers marksman.
He collected a pass from Shaun Newton on the right wing and powered towards the Leicester area, holding off the challenge of three City defenders before drilling a low drive beyond Walker.
Miller should then really have doubled his, and Wolves' tally, but fired wide from 12 yards 14 minutes from time.
It proved to be a costly miss as Benjamin calmly sent Murray the wrong way from the spot with a coolly taken penalty.