In the match held at the Foolad Shahr Stadium in Isfahan, two teams finished 2-2 after the extra time, and the game went to a penalty shootout.
Just two minutes into the match, Zob Ahan striker Morteza Tabrizi found the back of the net.
Vouria Ghafouri equalized the match in the 52nd minute.
Sepahan was reduced to 10-man in the 85th minute after referee Mohsen Torki showed Milad Sarlak his second yellow card for handball.
Mohammad Reza Hosseini gave Zob Ahan a lead in the 110th minute but Ghafouri scored again three minutes later.
In penalty shootout, holder Zob Ahan beat Sepahan 4-1 and qualified for the final match.
Esteghlal will play Naft Tehran on Wednesday in the semi-final.