Arsenal have not listed any Englishmen but Theo Walcott and Jack Wilshere are among the English under-21 contingent.
Wenger was delighted with his side's performance and was left to purr over 18-year-old Jack Wilshere's display in midfield.
But, after Daniel Sturridge nodded back a corner and Jack Wilshere helped it on, Smalling swept in the winner.
Arsenal's Jack Wilshere has been named in both the under-21 and senior squads.
The 21-year-old follows in the footsteps of Arsenal midfielder Jack Wilshere, who spent last season on loan at the Trotters.
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Arsenal will play second tier Brighton in the fourth round after edging out Swansea 1-0 courtesy of Jack Wilshere's spectacular strike.
Jack Wilshere should be fit for the Gunners after a back problem.
The Black Cats were almost made to pay as Jack Wilshere released Bendtner, only for Mignolet to claw the Dane's goal-bound shot over the bar.
With a trip to Manchester United looming on Saturday, Wenger made a double change with 19 minutes left, sending on Arshavin and Jack Wilshere for Eduardo and Eboue.
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Though Jack Wilshere's head-shaking trudge down the tunnel suggested otherwise, Wenger didn't believe he would have a hard a time picking up the team for the Bayern game.
The only blot on City's day came when captain Vincent Kompany was sent off for a sliding two-footed tackle on Jack Wilshere, though the Belgium defender appeared to win the ball.
But the north Londoners, despite the presence of Fabregas, Arshavin, Walcott and Jack Wilshere in their starting XI, were poor and their Championship opponents grew in confidence as the match wore on.
Jack Wilshere is one of those likely to come in to the Gunners' line-up, but the England Under-21 star admits he would consider a loan deal to gain more first-team experience this season.
Capello's squad announcement on Saturday included a call for Manchester City full-back Micah Richards, a player who had not featured in any of the Italian's previous squads while Arsenal duo Jack Wilshere and Kieran Gibbs were also named.
Wigan, unbeaten in five games at the DW Stadium, looked well in control but the catalyst for Arsenal's improvement finally came when Diaby left the field with a calf injury and Jack Wilshere came into the fray, bringing some much needed determination and urgency to lacklustre Arsenal.
On Twitter, tributes came from the likes of England footballers Jack Wilshere and Rio Ferdinand, Dragon's Den entrepreneurs Peter Jones, Duncan Bannatyne and Deborah Meaden, snooker star Jimmy White, former prime minister's wife Sarah Brown, television presenter Ben Shephard and teenage diving star Tom Daley, whose father died of a brain tumour earlier this year.
"Jack is a very gifted player with so much natural ability, " said Bolton manager Owen Coyle, who took Wilshere on loan last season.
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