Last man Moses Swaibu was shown the red card by referee Jarnail Singh after just 13 minutes for bringing down Le Fondre as he was through on goal.
Le Fondre picked himself up to beat Lincoln keeper Rob Burch from the spot for his 22nd goal of the season.
Imps boss Chris Sutton was forced to reorganise as Rotherham tried to take advantage of the extra man and Burch got down low to deny Millers winger Kevin Ellison a goal against his former club.
The 10 men showed great spirit and were inches away from levelling when a 30-yard drive from Brian Gilmour came back off the post.
Rotherham looked to have put the game out of sight after 65 minutes when Gary Roberts sidefooted past Burch after a quick counter-attack, but Lincoln staged a late fightback and grabbed a 77th-minute consolation through Steve Lennon’s first goal for the club.