Milner converted a 44th-minute penalty won by Fabrice Muamba to give Stuart Pearce's side, playing their first competitive fixture at Wembley, the edge at half time.
And Milner's Aston Villa team-mate Agbonlahor showed his trademark pace to fire t
he second in a victory that ensures England finish convincing winners of Group Three.
Agbonlahor had been struggling with a stomach bug, but was passed fit and took a more prominent role due to Theo Walcott's absence with the senior squad.
Pearce will have been satisfied by an encouraging display that saw England overcome a nervous start to stamp their authority on the out-fought Portuguese.
Chelsea defender Michael Mancienne almost nodded England ahead via a Fabrice Muamba free-kick but his header was just wide.
The effort preceded a period of English domination as Agbonlahor showed speed and strength to create a chance for Adam Johnson, who was denied by the fingertips of goalkeeper Rui Patricio.
Milner then fired England ahead from the spot.
Paulo Machado could have some justification for complaining that his penalty for clattering into Muamba was harsh, but Milner made no mistake as he rifled home in the 44th minute.
Milner broke into space early in the second half and tried his luck from long range, but this time Patricio was able to keep him out.
Patricio's workload continued to grow as he stopped a Tom Huddlestone free-kick that was headed for the bottom left.
Mancienne was proving a menace at corners and after another effort went wide he was pressed into action at his own end to disrupt Freitas' who had slipped free.
England's early woes became a distant memory as Agbonlahor fired Pearce's team further ahead.
Mark Noble sent Agbonlahor sprinting into space and, capitalising on poor positioning from Portugal's centre-backs, he slotted the ball beneath Patricio.
Substitute Fraizer Campbell replaced Agbonlahor and the Manchester United forward, on loan at Tottenham, set off a dazzling run that ended with a fine save by Patricio.
Portugal enjoyed a late flurry but Hart dealt with a pair of long-range efforts.
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