Shaikh Salman, who hails from Bahrain, received 33 of the 46 votes to sweep to victory ahead of Thailand's Worawi Makudi (7 votes) and Yousuf Al Serkal of the United Arab Emirates (6 votes) in the election at the AFC Extraordinary Congress.
"I congratulate Shaikh Salman for his thumping victory. I'm sure his endeavours will go a long way in developing and protecting Football in Asia," AIFF President Praful Patel said.
"I look forward to working together and exchanging footballing ideas and programmes in the near future," he said.
AIFF General Secretary Kushal Das said, "Indian Football has always been grateful to AFC for their support and we are confident that the 'Sleeping Giant' will stay on Shaikh Salman's priority list. I congratulate him for winning the elections for the post of the AFC President as well as the vacant post of FIFA Executive Committee member from AFC.