Sven-Goran Eriksson fielded a five-man midfield in support of Wayne Rooney, with skipper David Beckham in a holding role.
The opening minutes in Cardiff saw little goalmouth action, with Frank Lampard going closest with a long-range effort.
Midway through the first half Rooney and Steven Gerrard cut a swathe through the home defence but the former was denied by Wales keeper Danny Coyne, who also gathered Shaun Wright-Phillips' follow-up effort.
Ten minutes before the interval Ashley Cole had to head away from John Hartson following a deep Ryan Giggs cross and soon after the same combination almost gave Wales the lead.
The big striker met Giggs' centre with a superb downward header, but Paul Robinson made a world-class one-handed save to ensure the game was goalless at the break.
Wright-Phillips tested Coyne early in the second half and nine minutes in England made the breakthrough.
Beckham's long pass released Wright-Phillips and his ball in to Cole allowed the Chelsea midfielder to sidefoot past Coyne, with the aid of a large deflection off Danny Gabbidon.
Soon after, Rooney's deft chip forced a fine save from the backpedalling Coyne.
England then settled back to mop up the pressure and stood firm despite a late Wales onslaught to seal the win by the narrowest of margins.
Wales: Coyne, Duffy, Page (James Collins 64), Gabbidon, Partridge, Ricketts, Fletcher, Robinson (Koumas 55), Davies (Earnshaw 69), Giggs, Hartson.
Subs Not Used: Edwards, Roberts, Jones, Ledley.
Booked: Hartson.
England: Robinson, Young, Carragher, Ferdinand, Ashley Cole, Beckham, Lampard, Gerrard (Richardson 84), Wright-Phillips (Defoe 67), Joe Cole (Hargreaves 76), Rooney.
Subs Not Used: Upson, Kirkland, Neville, Bent.
Goals: Joe Cole 54.
Att: 70,715
Ref: Valentin Ivanov (Russia).