The autumn internationals were also marred by a series of collapsed scrums and Rowntree is expecting much better in the Six Nations.
He said: "The South Africa game was a big kick in the backside for them all round.
"They brought real physicality to the game, but what disappointed me in that game was the penalties which we conceded in the scrum."
"It's not good enough, particularly the engagement penalties.
"We were the least penalised scrum in the world then, so to concede three in that game was disappointing.
"Wales' front line are one of the best in the Six Nations, they are a real force.
"Down there on a Friday night, it'll be a seriously big test for us.
"I think you have to be confident going to a place like Cardiff, but by no means complacent.
"There are a lot of little battles that we are going to have to win, to win that ball.
"It pains me to see a scrum collapse. In fact - I demand it, of my England players, to keep a good shape in the scrum.
"I want them pushing players around, I don't want them to be on the floor all day - it's embarrassing when that happens.
"As protective as that sounds, that's the thinking going forward."