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Elliott, who was selected to replace the suspended Clinton Morrison, struck when Robbie Keane fought to recover possession in the Cyprus penalty area after Kevin Kilbane had put the defence under pressure with a good cross from the left.
Keane succeeded in knocking the ball away from a defender and Elliott beat goalkeeper Panayiotu with a left-foot shot on the turn from six yards,.
Ireland's great start was almost wiped out as Cyprus reacted with spirit.
Goalkeeper Shay Given had to make three outstanding saves in the following 15 minutes as Cyprus created openings with centre-forward Okkas in lively form.
It was Okkas who forced Richard Dunne into conceding a penalty in the 14th minute with some neat footwork in the penalty area. Okkas himself struck the penalty but Given made a magnificent save to turn the ball outside for a corner.
Cyprus were back immediately and Given again showed his capabilities with good saves from Michail and then again from Garpozis as Ireland struggled to control a quick and elusive Cyprus strike force.
Ireland were lucky to reach half-time still in front. They conceded possession all too easily to Cyprus and the Cypriots ruled the game in midfield.
Given stood between them and an equaliser as Cyprus controlled the game. He made yet another marvellous save when stretched high to pull down a clever shot from Okkas from 20 yards and over a crowded goalmouth in the 40th minute.
Ireland had to replace Steve Finnan at half-time and in the re-shuffle that followed Matt Holland came into central midfield, Damien Duff went to the right wing and Kevin Kilbane to the left.
Ireland showed improved form in the second half without ever playing with real conviction.
They were almost in for a second, however, in the 78th minute when Elliott found Robbie Keane inside the penalty area. Keane lobbed the advancing goalkeeper but defender Louka got back to clear the ball for a corner from virtually off the goal-line.
Ireland had more injury worries when Duff was forced off in the 60th minute to be replaced by Steven Reid and David Connolly came in for Robbie Keane in the 88th minute in what was obviously a tactical move.
Ireland were happy to hear the final whistle when they picked up three points that help to keep their hopes of qualifying alive.
Ireland: Shay Given; Stephen Carr, Richard Dunne, Kenny Cunningham, John O’Shea; Steve Finnan, Graham Kavanagh, Kevin Kilbane, Damien Duff; Stephen Elliott, Robbie Keane. Subs; Holland for Finna 46, Steven Reid for Duff 60, Connolly for Keane 88.
Cyprus: Panayiotu; Ilia, Lambrou, Louka, Garpozis, Michail, Makridis, Charalampidis, Alonefitis, Okkas, Konstantinou.