Mathieu Flamini gave Milan a 30th minute lead only for Goran Pandev to equalize three minutes later.
Gilberto's move means three midfielders have left Arsenal this summer, with Alexander Hleb (Barcelona) and Mathieu Flamini (AC Milan) also moving out.
To make things worse, Heskey was sent off with seven minutes later for a second bookable offence after he crashed into Mathieu Flamini.
BBC: SPORT | Football | Premiership | Birmingham 0-2 Arsenal
Then Arsenal lost Mathieu Flamini, arguably Arsenal's most consistent performer, when he picked up an injury during the Champions League quarter-final second-leg at Anfield.
Mathieu Flamini, 22, has proved to be an extremely capable left-back while Emmanuel Eboue, also 22 and brought to the club from Beveren in January 2005, has been sensational.
BBC: SPORT | Football | My Club | Arsenal | Why Arsenal came good in Europe
Midfielder Mathieu Flamini has been a huge bust since his summer 2008 arrival from Arsenal and, indeed, you feel he's only still here because Milan couldn't find any takers.
Look back through the years and you'll find folks like Mathieu Flamini and Gilberto Silva (2008), Thierry Henry (2007), Ashley Cole (2006), Patrick Vieira (2005) and Giovanni Van Bronckhorst (2004).
The marauding McFadden, who was playing on his own in attack after Mikael Forssell was sacrificed for defender Stuart Parnaby following the red card, was brought down by Mathieu Flamini.
Arsenal went into the game after a turbulent week which had seen the departure of Mathieu Flamini to Milan and rumours about the future of Alexander Hleb and other first-team players.
Gattuso and 59-year-old Scot Jordan had already clashed on the touchline during a bad-tempered second half in which Mathieu Flamini escaped with a only booking for a two-footed challenge on Vedran Corluka.
Gilberto has been kept out of the side because Cesc Fabregas and Mathieu Flamini have formed an impressive central midfield partnership to help steer Arsenal to the top of the Premier League.
The hosts improved after the break but it was still Milan who provided the threat, with Mathieu Flamini and Pato coming desperately close to forcing extra time as the home fans watched the clock counting down with increasing anxiety.
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