The hosts held firm for ninety-three minutes, but stumbled just before the final whistle...
Greece were the more active team in the early minutes of the game and a had a great chance through Kostas Katsouranis, but the midfielder's header did not trouble Haber in goal for Malta.
The Blue-White continued to press for the opener, but their finishing let him down on a couple of occasions. Katsouranis tried his luck with a powerful shot from just inside the box in the 16th minute, but saw his drive miss to the left.
The game became a bit too scrappy in the following minutes with a series of fouls in the centre of the pitch. The visitors had a decent chance through Nikos Liberopoulos in the 23rd minute, but Haber pulled off a good save.
The Malta goalkeeper had much more to do in the next couple of minutes as he had to intervene twice to prevent a goal. Dimitrios Salpigidis had a good shot saved by the shot-stopper as frustration was beginning to get the better of Greece.
Katsouranis had a couple of good opportunities for the Blue-White, and Andre Schembri and Daniel Bogdanovic went close for Malta, but neither team managed to score before the half-time whistle.
Greece continued to be the better side in the second half and were unlucky not to take the lead just two minutes into the second period when Katsouranis had a decent shot saved by Haber.
In the 54th minute the goalkeeper was once more the hero for Malta as Liberopoulos had a very good header saved and moments later hit the bar with another headed finish. Just before the hour mark Bogdanovic wasted Malta's best chance of the game as he took too long to shoot from the right side of the penalty are, just outside the six-yard box, and saw his finish blocked.
Liberopoulos had another shot saved by Haber in the 66th as Greece were looking increasingly likely to head home with just a point in the bag. Things took a turn for the worse as Milan defender Sokratis Papastathopoulos was given his marching orders from a bad tackle on Michael Mifsud in the 84th minute.
Torosidis had the final say, however, as he headed in the winner for Greece in the very last minute of the game after a misunderstanding in Malta's defence.
The victory sent the Greeks top of Group F after Croatia suffered a surprise defeat in Georgia. Malta remain bottom of the standings.
Follow Goal.com on . Get the latest football news direct... Check out Goal.com's page; be part of the best football fan community in the world!