City were happy to pull six or seven men back whenever danger threatened, but Rotherham gave a hint of what was to come when Kevin Ellison's 32nd-minute shot was brilliantly saved by Rob Burch.
And Burch was helpless five minutes later when Le Fondre latched on to a long punt out of defence and beat the keeper with a powerful shot for his 13th goal of the season. Le Fondre was denied a second goal when Burch made another stunning save in the 44th minute.
The visitors were largely restricted to long-range efforts and fell further behind with eight minutes remaining when Le Fondre converted Tom Pope's cross with a wonderful overhead kick.
The Millers striker was upended in the area by Janos Kovacs soon after, but failed to convert the resulting spot-kick.