Deon Burton bagged a brace against his former club to send the Gills five points clear at the top of League Two.
"It was a fantastic result and a fantastic performance for us," Allen said.
"Rotherham are a top form team at the moment and we have gone through a little patch where we haven't turned good performances into results and it has tested our resolve, but we have done the same work.
"Rotherham are a good team and at times it was backs to the wall and our keeper has made a couple of good saves and everyone on our team had to defend defiantly.
"But then when the chances came at the other end, that partnership of Danny Kedwell and Deon Burton is very, very dangerous so I was delighted with all our squad.
"They were good goals from Deon and he's been a good pro since he joined us and he looks after his body, trains and practices hard and you get those rewards when you do that."