The 25-year-old who has been impressive in front of goal since moving to midfield from defence scored his seventh goal of the season - six in the last five games - as the Millers missed the chance to climb out of the relegation zone.
After a goalless 45 minutes, Kenny McLean broke the deadlock to put the Canaries in front.
Ajayi, making his 38th league appearance for the Millers this season, levelled proceedings in the 52nd minute.
Five minutes later, Ben Godfrey scored the matchwinning goal to deny Paul Warne’s side a share of the points.
A win could have seen Rotherham - 22nd in the log - move out of the relegation zone after Reading played out a 0-0 draw with Stoke City.