Proctor damaged a leg after being knocked to the ground by Chris Solly but referee Trevor Kettle waved play on and it resulted in the visitors scoring their second goal.
Both sides were unchanged from the previous Saturday, having made numerous changes for the League Cup in midweek.
Jamie Proctor had an early chance for the Millers but hit a return pass from strike partner Kieffer Moore across the six-yard box and wide.
They were made to pay in the 16th minute when Jake Forster-Caskey curled out Charlton's second corner and centre-back Patrick Bauer headed back across Richard O'Donnell and into the net from eight yards.
Millers centre-back Semi Ajayi should have equalised when he raced in to meet a corner from Joe Newell but contrived to head wide from four yards.A full-length diving save from O'Donnell prevented Ricky Holmes making it 2-0 before the break.
Moore failed to control in front of goal and then elected to shoot rather than send in Proctor as Rotherham pressed after the break.
Charlton struck back and, after Solly's challenge on Proctor, Holmes crossed deep to the far post and Josh Magennis headed home in the 66th minute. After a lengthy delay Proctor was carried off.
Ahmed Kashi headed away from under his own bar as Joe Newell chipped the ball in but there was no way back for the Millers despite nine minutes of stoppage time.
Robert Gledhill's Analysis: Rotherham causing problems for themselves
The Millers must stop the habit of being the architects of their own downfall if they are to challenge for an immediate return to the Championship.
On the other hand, Charlton, relegated two seasons ago, already look capable of going back up.