Captain Massimo Ambrosini suffered a knee injury while striker Alexandre Pato pulled a leg muscle and both will now be out for around three weeks, the club said in a statement, meaning the pair will miss the next group game at Ajax.
Milan were woeful for an hour against the French side in their Group G opener before new striker Zlatan Ibrahimovic burst to life with two goals in three minutes.
The patchy performance followed last weekend's shock 2-0 league defeat at promoted Cesena and new boss Massimiliano Allegri wants the team to show more verve having mainly pinged pointless long balls forward during Wednesday's first half.
"It will be a very difficult game against Catania and because of this we need to recover our energy and physical force as quickly as possible," he told reporters.
Ambrosini's early exit allowed substitute midfielder Kevin Prince Boateng the chance to shine on Wednesday and he is likely to keep his place with Robinho coming in for Pato. Defender Thiago Silva should also return after injury on Saturday.
Champions Inter Milan had their own travails in Europe in midweek, drawing 2-2 at Twente Enschede, as they began the defence of their Champions League title in unconvincing fashion.
Next up is a trip to Palermo on Sunday where the intimidating crowd always makes life uncomfortable for visiting teams, even if their own side look toothless this term without injured striker Fabrizio Miccoli and the departed Edinson Cavani.
Inter look poised to be without forward Goran Pandev for around 10 days after his injury against Twente turned out not to be as bad as first feared but his absence will probably force a change in tactics for coach Rafael Benitez.
A switch to 4-3-1-2 from 4-2-3-1 is likely, pushing in-form forward Samuel Eto'o closer to goal and lifting the burden off the struggling Diego Milito.
Chievo, the only side with a maximum six points in Serie A, host promoted Brescia on Sunday, while Juventus search for their first win at Udinese.
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