Early goals by Frank Lampard (penalty) and Darren Bent secured a comfortable success in Group G of the European Championship qualifiers and Wayne was withdrawn with 20 minutes remaining.
"I decided for a new position for Rooney," admitted Capello afterwards. "When we are defending, he and [Aston Villa winger] Ashley Young are staying wide but, when we had the ball, they caused Wales problems."
The Reds striker did pick up a first-half booking that rules him out of the Wembley fixture with Switzerland in June.
Elsewhere, Darron Gibson helped Republic of Ireland to a 2-1 success against Macedonia. Our midfielder's free-kick was spilled by Edin Nuredinovski to allow West Ham loanee Robbie Keane to score what turned out to be the eventual winner.
Mexico striker Javier Hernandez just cannot stop scoring at the moment as he struck twice in the first half of his country's 3-1 win over Paraguay. Chicharito dived to head home a Pablo Barrera cross
Wales 0-2 England
Rep of Ireland 2-1 Macedonia
Mexico 3-1 Paraguay
Portugal 1-1 Chile
Ecuador 0-2 Colombia
Serbia 2-1 Northern Ireland
Luxembourg 0-2 France