The Spireites beat the Dons 1-0, but after the game admitted a charge of fielding an ineligible player, George Margreitter, and will now have to face Karl Robinson's side again.
Margreitter, who is on loan from Wolves, played in the fixture, despite not having completed the necessary paperwork in time.
In a statement released on the their official website, the FA confirmed that submissions from Chesterfield had been considered ahead of the decision to order a replay.
"Following an FA Cup sub-committee hearing at Wembley Stadium on Monday, Chesterfield have been ordered to replay their FA Cup Second Round Proper fixture against Milton Keynes Dons," the FA confirmed.
"Chesterfield had admitted a breach of FA Cup Rule 15(j), after fielding an ineligible player, namely Georg Margreitter, in their 1-0 win at MK Dons on Saturday 6 December 2014.
"Margreitter - on loan to Chesterfield from Wolverhampton Wanderers - played in the fixture without the necessary written permission having been received by The FA as at the 12noon deadline on Friday 5 December 2014.
"After considering submissions made by Chesterfield in relation to the charge, the committee has ordered the tie to be replayed at MK Dons on the earliest available date as decided by The FA.
"The tie will be played to a finish, with no further replay
No further action was taken against Chesterfield as ordering the tie to be replayed was deemed sufficient punishment.
"Full written reasons will follow.
"The decision is final and binding on all parties."
The winner of the replayed tie will face a trip to either Worcester or Scunthorpe in the third round.
Source : PA
Source: PA