The 20-year-old will stay with the Dons until February 21 and could make his debut against Sheffield United on Saturday.
Clarke-Harris, who is the Millers' record signing, has scored three goals this season.
“Jono is a young man we think extremely highly of. He is at a very early stage in his career which must mean him starting competitive first-team matches,” Boss Steve Evans said.
“The lad has been to see me on a number of occasions, perhaps at times frustrated, which is understandable given his youth. When an approach came in from a number of clubs challenging at the top end of League One, he had the option of three moves. We hope he can score some goals before coming back to the Millers to play an important part in the remainder of the season.” he added.