Rooney was booked for a foul on Joe Ledley just before half-time in England's 2-0 win over Wales at the Millennium Stadium on Saturday.
It was a costly caution because, as Rooney also collected a yellow card against Montenegro in October, he must now sit out an important game at Wembley on June 4.
"Rooney didn't realise,'' Capello said. "I just told him it was not a good booking. He said 'Why?' "He didn't remember that he got booked.''
It means Capello will have to make at least one change to his starting line-up for England's next competitive game, having regained the initiative in Group G thanks to early goals from Frank Lampard and Darren Bent.
The result ended a tortuous couple of weeks from the England coach, who has come under fire for the way he handled John Terry's reintroduction as captain in place of injured Manchester United defender Rio Ferdinand.
Not that Capello feels any sense of satisfaction.
"Why is it a vindication for me?'' he said. "I don't have anything to vindicate. It is my job. When we win we are the best, when we lose we are sh... This is normal.''
"It was a normal performance from Wilshere,'' Capello added. "His performances this season have been incredible. "He has improved an amazing amount in a short space of time. Arsene Wenger said the same thing. He played like someone of 29 with 40 caps. I hope there is more to come. Good players are always improving.''
Less has been said about Young and Parker, although it seems both men could be around for a while yet.
"Ashley Young is improving really well,'' Capello added. "This year he is a really good player. "He played very well against Denmark last month. He played very well today and he is also doing well for Aston Villa.
"Scott Parker was also good in that position just in front of the defence. He won back a lot of possession for us. He was always in a good position just in front of the back four all the time.''
There was never any question of who would win once England had established their two-goal cushion inside the first quarter of an hour.
Lampard drove home a fourth-minute penalty after Young had been brought down by James Collins, then Bent was on hand to score for the third consecutive game when he tapped home Young's cross after he had been released by Glen Johnson's brilliant long pass.
"I don't know if it is the best we have played,'' Capello said. "But I am happy because we played really well in the first 30 minutes.
"We pressed the ball. We won the ball back quickly and the movement of the players without the ball was really good. Everything was really nice. After this moment we had longer in possession but we still created chances to score.
"It was really difficult for Wales to get to our box. They only managed to do it at the end of the game.''