The AC Milan attacker was sent off for picking up two bookings in the space of four minutes, but the Azzurri held on to take another step forward on the road to Brazil
The Azzurri turned in a dismal performance in Prague and appeared in real danger of defeat when their star forward was sent off for a second bookable offence on 71 minutes.
However, the Czechs, who had repeatedly been frustrated by Gianluigi Buffon up until that point, missed a glorious chance to win the game when Petr Jiracek volleyed against the post, meaning the home side had to settle for a draw that leaves them third in the pool, a point behind Bulgaria.
Italy came into the game on the back of a four-game winning streak in Group B but the Czechs, who were routed 3-0 at home by Denmark in their last outing, made the brighter start and they really should have taken the lead 12 minutes in but Buffon saved brilliantly with his feet after the ball had fallen kindly for Jiracek in the area.
The hosts continued to look the side more likely to break the dealock during the remainder of a desperately underwhelming first half, but that was not saying much, given just how little the Azzurri were offering from an attacking perspective, with Balotelli the only player clad in blue who looked remotely capable of making something happen for the visitors.
As it was, though, the best that the Czechs could muster before a most welcome break from the tedium on the field was a decent long-range effort from Libor Kozak.
After making the rather surprise decision to play 4-3-1-2, with the unfortunate Riccardo Montolivo again employed in the trequartista role that he is in no way suited for, Cesare Prandelli even more bizarrely opted against reverting to his usual three-man frontline for the start of the second half, and instead simply replaced Stephan El Shaarawy with Sebastian Giovinco.
The change in personnel made little impact on the toothless nature of Italy's display and they were indebted to the brilliance of Buffon again on the hour when the captain saved well with his feet once more, this time from Kozak, who had been put in on goal by a perfectly-pitched ball over the top from Tomas Rosicky.
Kozak drew another smart stop from Buffon five minutes later, after evading Daniele De Rossi on the edge of the area as the hosts belatedly realised that they had an excellent opportunity to derail their group's runaway leaders.
Their hopes of doing just that were significantly boosted by Balotelli's dismissal, with the striker shown two yellow cards after two needless fouls in the space four minutes, though it must be said that the second booking, for throwing his hand in the face of Theodor Gebre Selassie, was harsh in the extreme.
Balotelli appeared to concur with that sense, as he lashed out at the tunnel in frustration as he marched away from the field of play.
The Czechs should have won it with six minutes left, but after Italy had completely switched off for a Jaroslav Plasil free kick, an unmarked Jiracek volleyed against the outside of the post, much to the relief of the Azzurri, who took another significant step on the road to Rio in spite of a dismal display.