Rooney missed the recent friendly against Croatia due to a minor knock but has since returned to club action with The Toffees.
He has proved his fitness to England coach Sven Goran Eriksson with the Swede naming the teenager in his party for the two crucial qualifying games.
Manchester United midfielder Scholes has been left out of the squad as his club boss Sir Alex Ferguson ponders sending the player for a hernia operation.
Ferguson was angered that Scholes's injury was aggravated while on international duty for the friendly with Croatia and will decide next week whether to send the player under the knife.
Scholes will be out for at least four weeks and faces a race against time to be fit for the decisive group tussle with Turkey at the start of October.
The midfielder's club colleague Gary Neville returns to the squad after injury but experienced Middlesbrough defender Gareth Southgate has not been recalled.
England face Macedonia in Skopje on September 6 before entertaining Liechtenstein at Old Trafford four days later.
Squad:
James (West Ham), Robinson (Leeds), Walker (Leicester); G Neville, P Neville, Ferdinand (Man Utd), Campbell, A Cole (Arsenal), Mills (Middlesbrough), Bridge, Terry (Chelsea); Beckham (Real Madrid), Butt (Man Utd), Murphy, Gerrard (Liverpool), J Cole, Lampard (Chelsea), Dyer (Newcastle), Hargreaves (Bayern Munich), Sinclair (Manchester City); Heskey, Owen (Liverpool), Rooney (Everton), Beattie (Southampton).
