Rooney showed his frustration as he trudged off the field in Cape Town, saying to a TV camera: "It's nice to see your own fans booing you."
But the Manchester United star was keen to put the record straight. "I am as passionate about the England team as anyone. Last night, on reflection I said things in the heat of the moment that came out of frustration of both our performance and the result," he said.
"The most important thing now is to regroup be positive and work towards winning the game on Wednesday. To do this the players will need the support of the fans more than ever. For my part I apologise for any offence caused by my actions at the end of the game."
England must beat Slovenia in their last Group C game on Wednesday to be sure of a place in the last 16.