Gianni Infantino wins FIFA presidency on Friday in second round of votes with 115 votes ahead of Sheikh Salman with 88.
The presidential election has skipped into a second round as Gianni Infantino led the first round of votes but did not gain a majority.
One of the candidates, UEFA General Secretary Infantino reached 88 votes ahead of Asian Football Confederation president Sheikh Salman bin Ebrahim Al Khalifa with 85 in the first round.
Prince Ali bin al Hussein of Jordan got 27 votes while former FIFA official Jerome Champagne took seven.
A candidate has to reach 138 votes of the 207 in order to win in the first round. Candidates will need to gain a majority of votes to be elected as president in the second round.
The landmark presidential contest has became an Asia v Europe battle between Sheikh Salman bin Ebrahim Al Khalifa and Gianni Infantino.
But former FIFA vice-president Prince Ali bin al Hussein is aiming to upset the odds and received a boost on Friday with the heavyweight backing of the United States and Australia.
Outsiders Jerome Champagne, an ex-FIFA official, and South African tycoon Tokyo Sexwale, have also been doggedly pleading their cause to the more than 200 delegations in Zurich.
The result is uncertain and experts say that football leaders will not be able to escape multi-national corruption investigations even with a new president.
Blatter, 79, will be the big absentee at the extraordinary congress in Zurich. The Swiss sports baron suffered a spectacular fall over the last nine months.
Swiss police, acting under US warrants, arrested seven FIFA officials in Zurich two days before his re-election last May.
Blatter has since been banned from football for six years for ethics breaches and could face criminal charges.
With sponsors holding back on deals and a controversial 2018 World Cup in Russia looming, Sexwale said on the eve of the vote that FIFA was a "broken house."
Infantino, general secretary of Europe's football bloc UEFA, and Sheikh Salman, president of the Asian Football Confederation, have offered starkly different paths for FIFA.
While promising reforms similar to those to be voted Friday, Infantino has proposed increasing the World Cup from 32 to 40 teams and to more than double the amount given back to the 209 national associations to more than $1 billion in total every four years.
Sheikh Salman, who is seen as closer to the FIFA old guard and has a bedrock of support in Asia and Africa, has said the proposal could bankrupt FIFA.
He said Thursday he would not "mortgage" FIFA's future to win votes.
The sheikh has advocated splitting FIFA into commercial and football divisions with himself as more of a figurehead president.
Each of the rivals has political problems.
Infantino was for seven years the right-hand man of Michel Platini, the UEFA president also banned for six years for ethics breaches.
Sheikh Salman, a senior member of Bahrain's ruling family, has faced tough questions about the clampdown on pro-democracy protests in the Gulf state. He has called allegations made by human rights groups "nasty lies."
Going into the election, the voting maths is dizzying for Infantino and Sheikh Salman. Both have expressed confidence, however.
The AFC and Confederation of African Football (CAF), which between them have 100 votes, have publicly said they are backing 50-year-old Sheikh Salman.
However, Football Federation Australia, a member of the AFC, said Friday it will vote for Prince Ali, who also received the backing of the United States.
'Time to change'
Europe and a big bloc of votes in the Americas are largely behind 45-year-old Infantino, who was publicly endorsed by Canada on Friday.
Prince Ali, a brother of Jordan's King Abdullah II, believes he has persuaded a significant number of countries to back him.
The election, the prince said "will decide if FIFA goes ahead as we want or if it spirals down."
The congress is also to vote on reforms proposed by a FIFA commission and backed by the body's executive committee aiming to re-establish its credibility.
There will be a 12-year term limit for the president and other top officials, and their salaries will be made public.
Executive committee members will also face greater scrutiny. Many of the 39 individuals now accused by US prosecutors of involvement in more than $200 million of bribes for soccer deals have held high office on the committee.
"The eyes of the world are on us," FIFA's acting president Issa Hayatou said, as he urged member nations to back the reforms.
FIFA's sponsors who are holding out on deals and prosecutors in many countries will be watching the result for signs of football's commitment to reform.
The sport's top leagues also want to see a revolution.
"If FIFA and the people in FIFA are not going to act on the message from the whole world that it is time to change... then the system fails," Jacco Swart, head of the Dutch Eredivisie professional league, told AFP after a briefing of the newly created World Leagues Forum.