Sheikh Salman secured 33 of the 46 presidential votes available from AFC member associations in Malaysia, to beat Yousuf Al Serkal of the United Arab Emirates (six votes) and Thailand's Worawi Makudi (seven votes) in a lop-sided election.
The result drew huge cheers from the auditorium with compatriot Sheikh Ali Bin Khalifa then announcing his resignation from the AFC executive committee so that Sheikh Salman could assume the presidency. Member Associations are only allowed one seat in the AFC exco.
The Bahraini replaces disgraced Qatari Mohamed Bin Hammam, who was banned for life by FIFA in 2011 amid allegations of trying to buy votes during the lobbying process to run the world governing body.
The AFC had been in limbo ever since, with China's Zhang Jilong's interim leadership beset by numerous matchfixing and graft scandals among member associations.
Dressed in a sharp grey suit and black tie, the softly spoken Sheik Salman took to the microphone and told the AFC Congress, FIFA President Sepp Blatter and UEFA head Michel Platini that the confederation had to reform and become more transparent.
"Today I'm proud and happy, proud and happy to see the Asia football family gathered together," he said. "Proud and happy to see our family united under one roof in the capital of Asian football.
"We need complete reforms, what we need is an AFC where decision makers are accountable," he added.
His candidacy had drawn outrage from two human rights groups in Bahrain who asked Blatter to withdraw Sheikh Salman from the vote, accusing the Bahraini royal of human rights breaches during the pro democracy uprising that began in 2011.
Sheikh Salman, the head of the Bahrain Football Association, has denied the groups' accusations that players were arrested, detained, abused, tortured and publicly humiliated under his direction for their role in the protests.
Praising the efforts of China's Zhang, who stepped in to fill the void left by Bin Hammam, Sheikh Salman called on AFC members to take the initiative in reform.
"You need to be part of an open, fair transparent dialogue in the future. Our acting president, Zhang Jilong, has started this dialogue successfully, we can be grateful for a man to take the role at a challenging time.
"Clean up the past and turn the page for the future, restore transparency and integrity."
Following the election, former AFC president Bin Hammam published a cryptic Tweet in Arabic, using a phrase that is usually reserved for offering condolences.
A disappointed Al Serkal, an ally of Bin Hammam, promised to work with Sheikh Salman for the good of Asian football after the humbling loss in an election he had said he was favourite to win.
"I will have to work with him and he will have to work with me," he said. "I'm not going to be a cause or a reason to create friction between my country or any other country.
"My job, my role, is to bring people together, that is the spirit of sports, the spirit of football."
Al Serkal did not say if he would run again in two years, but his chances appear unlikely without the support of the Olympic Council of Asia, whose backing helped elect Prince Ali Bin Al Hussein to the FIFA executive committee two years ago and now Sheikh Salman.
The shorter two-year term on offer to the winner of Thursday's vote was a result of Bin Hammam's exit. The Qatari was elected unopposed as AFC president for a third four-year term in 2011, leaving two years on that cycle.
Blatter said earlier it was time for Asian football to move forward.
"It is a historical day because it is a day of election, a day of election in your confederation that has been in a difficult situation during the past two years," the Swiss said.
"And together you have overcome all these difficulties and now you are in this situation where you are going to have a restart.
"But I would identify this restart as an intermediary restart because then the right start will be in two years in 2015 ... you have two more years to put your house in order."
Following the presidential vote, Sheikh Salman was then elected to FIFA's decision-making executive committee, securing 28 votes to Qatari Hassan Al Thawadi's 18.
Sheikh Salman had narrowly failed to unseat then-AFC President Bin Hammam from FIFA's ExCo in 2009; losing a hostile vote of AFC members 23-21, with two votes deemed invalid because they were spoilt.
Northern Mariana Islands were not given a vote as an associate member, while Brunei were approved voting rights after winning a motion at the start of the congress despite not taking part in the required two AFC competitions in the last two years.