Mohammad Nejadmahdi scored the only goal of the match with a header in the 28th minute.
Tractor created several chances to equalize the match but its strikers lacked the cutting edge.
The match was supposed to be held on Thursday at the Yadegar-e Emam Stadium in Tabriz but was postponed to Friday due to the heavy snowfall.
Sepahan moved up to third place with six points, one point behind IPL leader Gol Gohar.