For 78 minutes the visitors looked likely to pull off an upset against a virtual Italian reserve side until the Fiorentina front man's clinical finishes rescued Marcello Lippi's men.
Italy had already won Group 8 and ensured qualification for next year's FIFA World Cup™ finals in South Africa. With nothing riding on this match, coach Lippi took the opportunity to switch his team around and changed the entire starting XI from the side that drew 2-2 against Ireland on Saturday.
The game was no more important for Cyprus but they deservedly took a 12th-minute lead when Konstantinos Makridis ran into the area and squared to captain Yiannis Okkas who passed the ball into the net as Italy's centre-backs stood off.
It took the hosts 20 minutes to assert some authority but they created very little, their best chance before the break coming from a Gaetano D'Agostino free-kick on 29 minutes that the Udinese player curled just wide of the upright.
Lippi was clearly unimpressed and wasted no time in bringing on Mauro Camoranesi and Antonio Di Natale for Simone Pepe and Giuseppe Rossi at half-time. However, three minutes after the restart Efstathios Aloneftis crossed into the Italy box and Alessandro Gamberini's header found Chrysostomos Michail who met the ball on the volley to beat Federico Marchetti.
Finally Italy found some menace and Gennaro Gattuso brought a fine save out of Sofronis Avgousti from distance. Yet still the world champions were failing to exert any serious pressure and a desperate Lippi brought on Daniele De Rossi for D'Agostino.
That finally gave the hosts a lift and Di Natale beat his man only to then waste his good work with a tame shot straight at Avgousti. Fabio Quagliarella then crossed for De Rossi but Avgousti got down low to save his header on the line.
Di Natale stung Avgousti's finger-tips with a rasping strike from outside the box before Gilardino pulled a goal back 12 minutes from time from a Camoranesi cross. Three minutes later he snatched the equaliser from Quagliarella's centre.
Konstantinos Charalampidis then brought a flying save out of Marchetti seven minutes from time before Di Natale almost nutmegged Avgousti at the far post in a thrilling finish. But then in injury-time Gilardino slid in to poke Quagliarella's deflected shot over the line to complete the most unlikely comeback.