Stuart Pearce's national team protégés claimed an impressive 2-0 win over Portugal, which ensured a playoff place for the 2009 European Championships.
Villa's new recruit Milner put England ahead from the penalty spot just before the break, following a foul on Bolton's Fabrice Muamba.
And man of the match Agbonlahor, who defied a stomach bug to make the starting line-up, completed the scoring on 63 minutes.
The young striker used his lightning quick pace to sprint clear of the Portuguese defence and finish well.
Agbonlahor has constantly shone at Under-21 level and he, along with Milner, will now be looking to make the step up into Fabio Capello's side.