Monday's game at St Andrew's saw Smith - still looking for his first goal for the club - drop down to the substitute's bench, and Smith did not make it on to the pitch for the 1-1 draw.
Up to then, Smith - who has been hit with suspension this season, and remains one yellow card away from an automatic two-match ban - had never been an unused substitute under either Keegan or his predecessor Sam Allardyce, who signed him from Manchester United for £6m last summer.
But Keegan opted for a three-pronged attack of Michael Owen, Obafemi Martins and Mark Viduka, and when Martins was withdrawn, he was replaced by Charles N'Zogbia.
However, Smith - who left Old Trafford for regular first-team football at St James's Park - had no problem with the decision to leave him out of Keegan's starting XI.
Keegan told the Gazette: "Alan wasn't in theteam against Birmingham, but he's very much part of the team for me as far as I'm concerned.
"He's a great kid, and you wouldn't have known he wasn't playing the way he was around the dressing room.
"He's not the kind of player who goes sulking. He's a team player, and very much part of my plans."
Smith - who has made 30 appearance for the club this season - was hoping for a recall against Fulham at St James's Park this afternoon.
His absence from Keegan's Birmingham teamsheet - and that of Damien Duff, who was left out completely - were the main talking points among fans before the game, with Keegan making four changes from the side
beaten 3-0 at Anfield by Liverpool in the previous game.
And on Thursday Smith - a regular in Steve McClaren's England squads - was left out of Fabio Capello's provisional group of players for next week's friendly against France in Paris.
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