Le Fondre had endured a quiet second half of a tense game but took advantage of a defensive howler from Aaron Brown to put his side in pole position to book a Wembley final place ahead of the second leg at the Don Valley stadium on Wednesday night.
Ronnie Moore is expected to lead the Millers back into League One in his second spell in charge - but looked like he would be frustrated before Le Fondre's clinical late intervention.
For Aldershot, it was the biggest game since the club reformed in 1992 and a reminder of their participation in the first play-offs in 1987 when they beat Bolton and Wolves.
They will now need a fine away performance in Sheffield in the week but remain in the hunt for promotion.
Referee Andy D'Urso was quick to get into the action as he booked Shots midfielder Scott Donnelly for a late challenge on Pablo Mills inside five minutes before the home side crafted the first chance.
Donnelly was involved in some intricate build-up and when Dean Morgan fired the ball across the face of goal Marlon Jackson was inches away from converting at the far post.
Rotherham looked the more composed in possession and began to take charge as the half wore on, with Adam Le Fondre posing a constant threat up front.
Shots goalkeeper Jamie Young was then injured as he came out to collect a cross in front of Le Fondre so Venezuelan Mikhael Jaimez-Ruiz was called from the bench.
Le Fondre almost had the ball in the net moments later when he stretched to intercept a weak back-header from Andy Sandell but the prolific striker was unable to hook the ball home.
Dean Morgan almost snatched a goal at the end of the half when he outpaced a static backline but Andy Warrington did well in the Millers goal to race out and hack the ball away.
Rotherham centre-half Nick Fenton had a header cleared from the goalmouth at the beginning of the second period before the lively Dean Morgan shot over after a smart turn on the edge of the area.
Ryan Taylor then wasted the best chance of the evening on the hour mark.
Rotherham right-back Mark Lynch cut inside onto his left foot and delivered a great cross to the back post. Taylor was onside and unmarked six yards out but steered his header wide.
It was a huge let-off for the hosts and Anthony Straker almost volleyed them into the lead moments later with an acrobatic effort which drifted narrowly wide.
Straker then drove another shot across the face of Warrington's net before Le Fondre stole in in the 88th minute.
Brown failed to look before playing a backpass from near the touchline and instead presented Le Fondre with a clear run at goal.
Jaimez-Ruiz sprinted out to narrow the angle but Le Fondre calmly clipped the ball past him and into the corner.