Salman, a controversial candidate accused of being complicit in human rights abuses involving players in his country, trounced his opponents to win in the first round of voting in Kuala Lumpur.
The sheikh is viewed as a Blatter ally and his victory could prove significant if the 77-year-old FIFA president follows up his hints that he might change his mind and decides to stand for another term in 2015.
Blatter was quick to congratulate Salman on a "brilliant election" and added: "One of the key missions he will have to ensure is that unity prevails within the AFC."
Salman - who had denied the accusations from human rights groups - received 33 of the 46 votes to win a landslide victory, one which sounds the death knell for any remaining loyalty to his predecessor, Mohamed Bin Hammam, banned for life in December for "conflicts of interest".
FIFA had taken the unusual step of intervening in the election contest to warn that associations were not allowed to entertain any lobbying from Bin Hammam, once Blatter's most loyal supporter who later turned opponent and challenged him for the presidency.
Salman clearly benefited to an extent from Blatter's implicit if not explicit support in his campaign, and there will have been extra satisfaction for the FIFA president in that Salman also defeated Bin Hammam's fellow Qatari Hassan Al-Thawadi - head of the 2022 organising committee - in the election for the FIFA executive committee.
After an election campaign notable for its bitterness and mudslinging, Blatter issued a call for unity.
He said: "Unity, as well as solidarity, are absolutely key and necessary pillars for any institution to build solid plans and structures for its future. With two thirds of the world population, Asia clearly plays a huge role in the international football community. But it certainly has not yet reached its full potential. AFC shall unite all its energies to continue to strengthen the growth of the Game in Asia."
Salman will serve a two-year term until the next AFC Congress in 2015.