The Manchester United star signalled that he wanted to come off a couple of minutes before the end of the triumph, though Capello rejected the idea because he had used all six permitted substitutes.
However, the England coach reported afterwards that Rooney was merely suffering from a minor neck problem.
"He said he had a small problem in his neck but it is not a problem," said Capello.
"He wanted to come off for the last two minutes but I had made all the substitutions so it was impossible to change.
"Rooney is okay. At this moment he just needs to play and find his form."
Any injury to his talisman would have been an unwanted post-script to a strange game for Capello.
On one hand, a clear victory against a side ranked 17th in the world was reason to cheer, on the other issues must be addressed given Mexico were the better side, especially during the first half, in which they were unfortunate to end up behind.
Central midfield was a particular area of concern. The partnership of James Milner and Michael Carrick did not work and it was not until Capello moved Steven Gerrard into a more central position after half-time that England finally managed to exert some authority.
"I wasn't upset at half-time but I spoke with the players and told them what they had to do," said Capello.
"Mexico are technically very good. They are faster than us and it was not easy getting the ball back.
"Not all the teams we play against will be like this. But it is very important to press the ball and win it back quickly."
The performance of Gerrard in central midfield will have given Capello something to think about, especially if Gareth Barry fails to come through tests on his ankle injury tomorrow that could rule him out of the entire World Cup.
"We never suffered a lot during World Cup qualification but this time, I put two different players in, Milner who has played in midfield this year, and Carrick.
"I changed it after half-time and put Steven in the middle, where he played very well.
"He is a really good player and can play in midfield, as a number 10, in lots of different positions.
"Gerrard can play in midfield with Frank Lampard but we have to wait and see which players will be fit."
Peter Crouch scored his customary goal - his 21st, putting him joint 16th on the all-time England scoring list - and Glen Johnson found a brilliant effort to break his international drought.
However, it was returning central defender Ledley King who opened England's account, nodding home Crouch's lay-off from six yards.
Not that the Tottenham skipper was entirely happy with his contribution.
"I wouldn't say it was one of my better games but the more I play, the fitter I can get," he said.
"I have played three games in 10 days already this season, so why would it be a problem again?
"The medical staff are doing a brilliant job. It's now down to the manager to see who he picks. I will just do the best I can and see where it goes."
Capello was more forgiving in his assessment of King's contribution, although stating the defender will not be part of his starting line up for Sunday's encounter with Japan in Graz.
Aside from Barry, Capello has only one injury, Darren Bent, who sat out Monday evening's game with a hamstring problem.
The England coach realises improvements must be made, although he refused to state a generally down-beat atmosphere was in keeping with his own mood less than three weeks before the Group C opener against the United States on June 12.
"I am not concerned by tonight," he said.
"It was really important to know where we are now, physically and mentally after a long season.
"We have time to recover a lot of the spirit of the team and the qualities we have.
"When we play counter-attacking, we are really dangerous. But I don't just want to play on the counter. I want more."