Hayes made a double substitute at the break, with England and Spence making way for Harder and Kerr.
The Blues nearly made an immediate impact following the interval as Andersson delivered a free-kick in the box but an unmarked Bright missed the target with her header.
Chelsea came even closer moments later and this time it was a header from Eriksson, but Leicester forward Jess Sigsworth cleared the ball of the line to deny the Blues.
Kerr rose highest to meet a cross from Kirby, but the Australians close-range header was superbly saved by Foxes goalkeeper Levell.
The Blues were then denied by Levell once again as Reiten pulled the ball back to Harder in the box, but her low effort was saved by the legs of Levell.
Harder curled an effort just over the bar before Cuthbert found some space on the edge of the box but the midfielder fired her strike off target.
Chelsea finally broke the deadlock with eight minutes remaining.
Fleming, who had been impressive throughout, picked Harder out with a low ball into the box and the Denmark captain provided a clinical finish into the bottom corner.
After waiting 82 minutes for the opener, Chelsea added a second in stoppage time. Kirby raced onto a flick on from Kerr and the No.14 took one touch and slotted past Levell to seal the three points for the Blues.