Sheikh Salman beat Yousuf Al Serkal of the United Arab Emirates and Thai Worawi Makudi in the vote in Kuala Lumpur, and becomes the successor to the disgraced Qatari Mohamed Bin Hammam, who was banned from football for life by FIFA in 2011.
An AFC statement said: "Sheikh Salman bin Ebrahim Al Khalifa has been elected as the new AFC President following Thursday's election at the AFC Extraordinary Congress.
"Sheikh Salman received 33 of the 46 votes to sweep to victory ahead of Thailand's Worawi Makudi (7 votes) and Yousuf Al Serkal of the UAE (6 votes)."
A fourth candidate, Hafez Al Medlej of Saudi Arabia, withdrew on Wednesday night after gaining little support.
Sheikh Salman will serve a two-year term until the next AFC Congress in 2015.