The 29 year old centre back was forced off after just 16 minutes of the game at Windsor Park and was replaced by Chris Baird.
The game finished 1-0 to Northern Ireland, with Warren Feeney scoring his second goal in as many games for the hosts to take his country to top of Group 3. Elsewhere in the group, Poland thumped San Marino 10-0.
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Veliche Shumulikoski played the full 90 minutes for FYR Macedonia as they lost 4-0 at the Amsterdam ArenA.
Liverpool striker Dirk Kuyt scored twice in the first half with the other goals coming from Klaus Jan Huntelaar just before the half hour mark and Rafael Van Der Vaart in the second half.
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Alex Bruce, like Saturday, did not make the Bench for the Republic of Ireland as they drew 1-1 with Italy at the Stadio San Nicola.
Giampaolo Pazzini was sent off after four minutes for an elbow on John O'Shea, however the hosts took the lead after ten minutes through Vincenzo Iaquinta. Robbie Keane scored the equaliser for the Republic in the closing stages.
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