Wilshere played in the senior side's friendly international success over Hungary two weeks ago, replacing Steven Gerrard for the closing stages of the contest.
However, Stuart Pearce has named the Arsenal midfielder in his Under-21 squad for the qualifying matches against Portugal and Lithuania.
Head coach Pearce said: "Jack's had the experience of an international cap with the seniors and his development will come.
"Like Theo Walcott, I think having the experience of playing with the Under-21s and seniors will be a help to him and is something he will have to come to terms with.
"He shouldn't feel disappointed that he's been in the senior squad and then come back to the Under-21s and that's the mentality he has to come to the squad with."
Everton midfielder Rodwell and Manchester City defender Micah Richards, who were also hoping to feature in England's opening Euro 2012 qualifying matches against Bulgaria and Switzerland next month, have also been named in Pearce's 24-man Under-21 squad.
However, Arsenal defender Kieran Gibbs - who figured in England's defeat of Hungary, also as a second-half substitute - appears to be in line for another senior call having been left out.
Pearce added: "It's the strongest squad we could have got at this stage of the season. Kieran Gibbs aside, we're looking pretty strong.
"I was very impressed with the contribution of the players in the last match and the majority of those players are in, with one or two additions on top of that."
Liverpool defender Martin Kelly, Blackburn defender Phil Jones, Sunderland midfielder Jordan Henderson, Wigan striker Victor Moses and Aston Villa winger Marc Albrighton retain their places following their debuts against Uzbekistan earlier this month.
Albrighton's Villa team-mate Nathan Delfouneso is also back in the squad after making a goalscoring debut for Pearce's team against Greece in March.
There is also a first call for highly-rated Huddersfield goalkeeper Alex Smithies, who has previously been capped at Under-17 and Under-19 level.
Pearce explained: "He's had a lot of experience at Huddersfield over the last couple of years and is a goalkeeper who can play again in the next campaign for us.
"We feel he has done extremely well when we've seen him and even though he's young, he's played a lot of matches which is similar to Joe Hart when he was playing for Shrewsbury for a couple of years before he went to Manchester City."
England play Portugal in Barcelos on September 3 before facing Lithuania four days later at Colchester's Weston Homes Community Stadium.
England Under-21 squad:
Fielding (Blackburn), Loach (Watford), Smithies (Huddersfield); Bertrand (Chelsea), Jones (Blackburn), Kelly (Liverpool), Mancienne (Chelsea), Richards (Man City), Smalling (Man Utd), Walker (Tottenham); Albrighton (Aston Villa), Cleverley (Man Utd), Cork (Chelsea), Henderson (Sunderland), Lansbury (Arsenal), Moses (Wigan), Muamba (Bolton), Rodwell (Everton), Rose (Tottenham), Wilshere (Arsenal); Carroll (Newcastle), Delfouneso (Aston Villa), Sturridge (Chelsea), Welbeck (Man Utd).