The AC Milan striker headed home from Andrea Pirlo's 35th-minute corner before substitute Balotelli added a second at the death to finally kill off Ireland's brave resistance in Poznan.
Spain's 1-0 win over Croatia in Gdansk meant the reigning champions topped Group C, but Italy went through in second place.
On a night when only victory would do for Cesare Prandelli's men, they came up with the goods against an Ireland side whose exit from the competition was confirmed last week.
But while Italy dominated for long periods, they were unable to find a way past the green shirts for a second time to leave the Republic, led by winger Damien Duff on his 100th appearance for his country, in with a chance until Balotelli eventually calmed the nerves.
Giovanni Trapattoni's side, who had midfielder Keith Andrews sent off late on, staged a late blitz on the Italian goal which came up only just short, and although they restored some of their battered pride, they will return to Dublin tomorrow having failed to collect a single point.
Duff and his team-mates ran out wearing black armbands to mark the 18th anniversary of the shootings of six men in Loughinisland, County Down, as the victims watched the national team play Italy at the 1994 World Cup finals in the United States.
That day, Ray Houghton's goal secured a famous victory over the Italians, and the latest generation set out in determined fashion in an attempt to repeat the feat.
They might have taken the lead straight from the kick-off when Kevin Doyle ran on to Pirlo's careless pass, but defender Giorgio Chiellini dispossessed him before he could shoot.
Ireland safely negotiated the opening five minutes which had previously proved so problematical in the tournament, but as the deep-sitting Pirlo started to pull the strings, found themselves having to defend for dear life.
But where that had been beyond them in their opening two games, this time they found the resilience and organisation which had brought them to the finals.
The two sides traded blows in their own particular fashions, the Italians stylish and patient, the Irish more direct and abrasive, but with neither goalkeeper being called upon at all.
Richard Dunne and Sean St Ledger both had to get in good blocks to prevent Antonio Di Natale from troubling Shay Given, and the Leicester defender had to be on his toes to dispossess the same man as he threatened to carve his way into the penalty area once again.
But with 10 minutes of the first half remaining, Italy started to turn the screw.
Glenn Whelan's misplaced pass allowed Cassano to pick out Di Natale and when he rounded Given on the right side of the penalty area and shot from a tight angle, St Ledger once again came to the rescue on the line.
But the reprieve was only temporary and after Given had conceded a corner by spilling Cassano's snapshot, Prandelli's men edged ahead.
Pirlo's near-post delivery was met with a glancing header by Cassano and although Given got a hand to it, he could not keep the ball out of the net.
The sense of relief among the Italian fans, who were dwarfed in number by their Irish counterparts, was palpable, and will have been shared both on the pitch and the bench.
However, Prandelli's players returned knowing they still had to get through another 45 minutes and hope things elsewhere continued to go for them if they were to progress.
It would have been 2-0 within three minutes of the restart had St Ledger not once again denied Di Natale with a vital block, and Given had to get down well to keep out Cassano's side-footed effort seconds later with Italy looking to kill the game off.
Daniele De Rossi curled a 51st-minute shot over the angle of bar and post with Ireland looking more open than they had at any point until then.
But there was a flicker of hope for the Republic when Robbie Keane forced Ignazio Abate to concede a corner which Dunne headed wide.
Given had to repel another Di Natale effort at his near post with 55 minutes gone, but Andrews tested Gianluigi Buffon from distance for the first time on the hour.
Sensing that their time had come, the Republic launched a sustained assault on the Italian goal, prompting Prandelli to introduce wild card striker Balotelli with 15 minutes left on the clock.
But Buffon had to be at his best to keep out Andrews' drilled 79th-minute shot from Duff's back-heeled free-kick, with Ireland throwing everything they had at Italy.
However, it all turned sour at the death as Andrews, who had earlier been booked for a foul, received a second yellow card for dissent seconds before Balotelli hooked home a Pirlo corner to secure the win.
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