East Bengal's James Moga came off the bench to cancel out Padang's Edward Junior Wilson first half strike to edge past the Indonesian outfit 2-1 on aggregate courtesy the red and gold brigade's 1-0 win at home last Tuesday.
AIFF President Praful Patel lauded the Kolkata outfit for their achievement.
"I congratulate East Bengal Club for their historic triumph. I wish them luck for the semifinals," Patel said.
"This is a tremendous achievement. East Bengal until this match had won all their matches which speaks volumes about their performance at the International Level. This is a proud moment for Indian Football. I wish them all the very best for the semifinals."
East Bengal become the first Indian club since Dempo (in 2008) to reach the last-four stage of the AFC Cup, which is equivalent to Europe's Europa League.