McQuoid, who was handed his debut in the friendly against Morocco in November, will provide attacking cover after David Healy was suspended for the match following a yellow card in the 2-1 defeat to Serbia on Friday.
Rangers frontman Kyle Lafferty, who left the pitch after 45 minutes of that match, is also struggling with a knee problem, leaving manager Nigel Worthington with just Warren Feeney and Liam Boyce definitely fit and available for the Group C clash.
McQuoid has six Northern Ireland Under-21 caps and has scored 12 goals this season, all for former club Bournemouth and none since his January move to Millwall.
Worthington has other injury concerns ahead of the Slovenia match, one his side must win if they are to keep alive their hopes of qualification.
Captain Aaron Hughes is a doubt after dislocating his shoulder in Belgrade, although he played the full 90 minutes, while Jonny Evans has a groin problem.
Defeat in Belgrade ended Northern Ireland's three-game unbeaten run in qualifying, making the road to Euro 2012 all the harder in the process.