England were 2-0 ahead with five minutes to play and easing to victory despite a laboured performance at Wembley when they allowed Slovenia a consolation goal through Zlatan Ljubijankic whose near-post diving header beat goalkeeper Robert Green.
"I was quite pleased with the performance, but I was not happy with the last four or five minutes," said Capello.
"I want players to be focused and to concentrate from the first minute to the last but we played too slow, we played the long ball, it was not the style I like."
England will qualify for the World Cup in South Africa next year if they beat Croatia in a Group Six qualifier on Wednesday and that match will be played at a completely different pace to Saturday's warm-up which resembled a training game in patches.
Capello still saw value in the performance, though, saying: "I was pleased overall. Slovenia are a good team, with very fast strikers. They play similarly to Croatia and I learnt a lot from this game."
The Italian, who is likely to stick to his preferred first choice pairing of Emile Heskey and Rooney, added: "He (Defoe) always scores when he comes on in the second half."
"This match proved to be a real test before our qualifier against Poland (in Group Three) on Wednesday but although I am disappointed about the penalty, these things happen in football.
"But I am more angry over the injury to Cesar. I'm not angry with Rooney, I'm angry the injury happened in a friendly.
"We have probably lost him for Wednesday's match.
"He has had an x-ray and there is no break but the ankle is very swollen. We will see if he can play," he added.
