Rotherham manager Alan Stubbs felt midfielder Lee Frecklington was fouled in the build-up to the goal.
He said: "There is no doubt about it (the foul). If you look at the replay, it's pretty obvious, there are two hands on 'Frecks' which makes him go to the floor.
"We have taken the game to Newcastle and, if I am being honest, it has been a pretty uncomfortable 90 minutes for them."
Rotherham performed well in the game and hit the woodwork in each half through Jon Taylor and Dominic Ball's deflected effort in the final five minutes.
Stubbs feels his side are improving.
He added: "We are certainly getting better. On Tuesday we could have taken a point and today one bit of quality has been the difference between the two teams.
"When you're down there a little bit of luck deserts you but you have to make your own luck in this game. There were positives out of the display but not out of the result. For me it was a step in the right direction.
"If they keep performing like they have done in the last couple of games then it won't be long until they start picking up points. I've got no doubts about that."