The defender headed home from close range in the fifth minute of added-time as Greece replaced Croatia as leaders after Slaven Bilic's side suffered a shock 1-0 defeat in Georgia.
Greece had Sokratis Papastathopoulos sent off for a professional foul on Michael Mifsud with six minutes left.
Fernando Santos' side created several good chances but struggled to break down Malta's stubborn resistance on a frustrating night at the Ta' Qali National Stadium.
However, Torosidis' late goal was enough to take Greece top of the standings with 11 points from five games. Croatia are second with 10 points while Georgia are a further point adrift in third place. Malta remain bottom without a single point.
Greece were unlucky not to open the scoring early in the second half when striker Nikos Liberopoulos went close with two headers in the space of a minute, the second hitting Malta goalkeeper Justin Haber's crossbar.
Haber also produced a smart save to keep out Kostas Katsouranis's low drive on the hour as the visitors continued to search for a breakthrough.
Greece were reduced to 10 men in the 84th when Papastathopoulos felled Mifsud as the home striker threatened to break clear on the counter-attack.
But frustration turned to jubilation when Torosidis flicked home a mis-hit shot by substitute Kostas Mitroglou from Giorgos Karagounis' left-wing corner.
The teams meet again in their next qualifying match in Athens on 4 June with Greece first facing Euro 2012 co-hosts Poland in an international friendly on Tuesday.
