Sepp Blatter was voted in for four more years as FIFA president - but only after his rival inflicted a "bloody nose" on the 79-year-old.
More than a third of FIFA's 209 associations voted for Prince Ali Bin Al Hussein of Jordan as significant numbers turned against Blatter following the crisis that has struck the world governing body this week.
Blatter won by 133 votes to 73 to win a fifth term of office, but he failed to gain a two-thirds majority which would have seen him win in the first round. Prince Ali, the 39-year-old Sandhurst graduate, then withdrew from the contest rather than force a second round of voting.
The election in Zurich was held amid the continuing fall-out from the arrest of seven FIFA officials in the city and a total of 18 people connected to football indicted on corruption charges by the US justice department.
Football Association chairman Greg Dyke told Press Association Sport afterwards: "This was a bloody nose for Sepp Blatter."
The outcome is also set to see further protests from UEFA - the first action has come from David Gill, the Football Association vice-chairman who will reject the post of British vice-president as he does not want to serve under Blatter.
Gill will not attend the post-Congress executive committee meeting on Saturday, where a decision is set to be taken on the allocation of World Cup places to each confederation.
John Delaney, chief executive of the Football Association of Ireland, believes the latest scandal will mean Blatter does not see out his four-year term.
He told Press Association Sport: "I still think this is the beginning of the end of Sepp Blatter.
"I don't see him seeing his four years out - the momentum is too great. We now have to see how best we can use the European muscle. "
Blatter had told the 209 associations who gathered for the FIFA Congress that the crisis would not have happened if countries other than Russia and Qatar had won the vote for the 2018 and 2022 World Cups.
In what appeared a reference to the United States and England losing out, Blatter called for unity .
Most of the media investigations into FIFA have come from Britain, while it is the US justice authorities whose actions led to the indictments of 18 people, including charges that a FIFA bank account was used to channel a 10million US dollar (£6.54million) World Cup voting bribe.
Blatter said: "If two other countries had emerged from the envelope I think we may not have these problems."
Russia president Vladimir Putin on Thursday criticised the American indictments and claimed they were designed to undermine Blatter's re-election.
The Swiss added of the police swoop on the seven FIFA officials: "I am not going to use the word coincidence but I do have a small question mark."
He admitted the events of this week "unleashed a storm'' ahead but appealed to delegates for unity and said : "I am being held accountable for the current storm, okay so be it - I will shoulder that responsibility.
"I want to fix FIFA together with you - tomorrow, day after and in the weeks to come."
Blatter also hinted this term would be his last, saying: "At the end of my term of office I want to hand over a strong FIFA." He had given a similar message in 2011 however, only to change his mind and stand again.
Prince Ali had directly addressed the crisis that has struck FIFA and called for a "new dawn" for the world governing body.
He told delegates: "The eyes of the world are upon us and not for the first time and this time everything is at stake - for the game, for the world.
"We have heard in recent days voices describing our FIFA as morally bankrupt and an avaricious body which feeds off the game we love.
" There are no easy answers and no blame can be passed that washes away the stain.
''I will not hide among your ranks when things are bad and step forward when things are good. Now is the time to show the outside world that we are hungry for their respect."
Swiss police had earlier cleared the congress hall following a bomb threat. There was a another security incident when two pro-Palestinian protestors were ejected from the hall, while a demonstration calling for Israel to be ejected from FIFA continued outside.
The Palestinian FA dropped a proposal to have the Israeli FA suspended from FIFA but won the right for a committee to be established to ensure free movement of players and goods - and for FIFA to pass it to the United Nations to decide whether five Israeli settler clubs should be permitted to continue in "occupied territories".
This was followed by a symbolic handshake between the presidents of the Israeli and Palestinian FAs.
Source: PA
