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However, the Bosnians may feel that they were unlucky not to have taken the lead earlier in proceedings.
In the 21st minute Miralem Pjanic found Edin Dzeko with a slide-rule pass and the Manchester City frontman calmly slotted past Vincent Enyeama, but his effort was disallowed for an offside flag. Television replays appear to show that Dzeko was played onside.
Nigeria, though, looked far better than in their first game against Iran and had some joy attacking down the right-hand side where Emenike demonstrated pace and power.
The Super Eagles almost put daylight between themselves and Bosnia when Ahmed Musa worked himself some space, but his low drive failed to beat Begovic at his near post.
On the stroke of half time, the European side had a great chance to equalise when Pjanic pulled the ball back to Dzeko, but he failed to get his body over the shot and skied his effort.
Bosnia will be knocked out of the tournament if they lose this evening.