Chris Baird, Grant McCann, Damien Johnson, Steve Davis and McGinn will form a five-man midfield.
Such was Malbranque's first-half dominance that Fulham right-back Chris Baird was replaced at half time by Volz.
Schwarzer then produced another superb save to push away Yakubu's diagonal shot and Chris Baird cleared the ball.
Maik Taylor, Chris Baird, Corry Evans, Sammy Clingan and Grant McCann all pulled out of the squad on Wednesday.
Lafferty got on the end of a Chris Baird cross but his header lacked power and was kept out by Aouate.
Chris Baird dragged his shot wide before debutant Craig Cathcart put in a last-ditch tackle to deflect Ljubijankic's effort over the bar.
Northern Ireland wasted two opportunities to draw level within minutes of the goal with Chris Baird and Evans heading wide from close range.
The 20-year-old Manchester United player, currently on loan at Plymouth Argyle, came in following the withdrawal of injured pair Jonny Evans and Chris Baird.
Defender Chris Baird is suspended for the first game against Poland.
McIlroy started with three debutants in Tommy Doherty, Chris Baird and Andy Smith and he will not have been too disheartened following a spirited NI display.
Mirnes Sisic fired wide after five minutes, while Slovenia also had a penalty appeal turned down when Chris Baird appeared to push Zlatki Dedic to the floor.
Northern Ireland midfielder Steve Davis pulled out of the game late on Tuesday due to family reasons - Chris Baird was promoted from the bench to replace the Rangers player.
Both sides made changes at the break, Fulham bringing on Chris Baird for Pantsil and Wolves introducing Steven Fletcher for goalscorer Van Damme, and the hosts were level within four minutes of the restart.
The first opportunity of the match came when a long ball from Chris Baird found Diomansy Kamara, who controlled on the edge of the six-yard box, swivelled and forced a good save low down from Carson.
The Cottagers, who will be without suspended right-back Chris Baird for the second leg, must be admired for the way they held firm to the end, Schwarzer thwarting an angled effort from substitute Mladen Petric on 88 minutes.
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