They will play Chinese champions Guangzhou Evergrande who completed an 8-1 aggregate thrashing of Japan's Kashiwa Reysol earlier on Wednesday.
Seoul's win means there will be a Korean team in the final of Asia's premier club competition for a fifth straight season, with three of the previous four proving victorious.
The foundation of the semi-final victory by the Korean champions came on home soil last week, when they avoided conceding an away goal in a 2-0 success as Esteghlal suffered key suspensions.
The Iranians were without midfield duo Javad Nekonam and Andranik Teymourian for the second leg on Wednesday and so tried to get the ball forward to captain Farhad Majidi as quickly as possible.
The more technically efficient Seoul opted for a swift passing game and both sides created numerous opportunities in an entertaining first half before Ha opened the scoring with a sumptuous finish.
The midfielder wriggled free of Ahmad Jamshidian before clipping a left-foot shot from just outside the area over the Esteghlal goalkeeper into the top corner of the net.
Esteghlal brought on target man Mohammad Ghazi at the start of the second half as they went in search of the four goals required to advance and he forced the corner from which the Iranians levelled the match in the 50th minute.
Former Aston Villa defender Jlloyd Samuel stretching to head home and spark belief of an unlikely fightback in the stands.
The goal only increased the attacking efforts of both sides with Seoul's Montenegrin striker Dejan Damjanovic guilty of missing two great opportunities to make the tie safe near the hour mark.
Those misses looked costly when Ghazi put the home side in front in the 76th minute by calmly slotting in a rebound after his initial effort came back to him off the post.
Seoul were rewarded for sticking to their attacking philosophy as fullback Cha Du Ri was brought down in the penalty area in the 79th minute, with Kim confidently lashing home the spot kick despite a laser being shone in his face.
(Reporting by Patrick Johnston in Singapore; Editing by Clare Fallon)
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