The 75-year-old Swiss was the only candidate in Wednesday's election, with the English and Scottish Football Associations failing to delay the vote.
They wanted a postponement amid allegations of corruption within Fifa, but were only supported by 17 of the member associations.
Blatter won re-election with 186 votes from the 203 member associations and he will be in charge until 2015.
"I thank you for your trust and confidence from the bottom of my heart," said Blatter, who was applauded back into the auditorium by the rest of Fifa congress after his unchallenged victory in Zurich.
"Our pyramid is intact, the base, the foundation is strong and together we have four years to continue on our path and do our job.
"We will put Fifa's ship back on the right course in clear, transparent waters. We need some time to do it, but we shall do it.
"Today something marvellous happened and I'd simply like to tell you I'm deeply moved and honoured. It's a challenge, a new one for me, and I accept it."
Later in the day, in his closing statements, Blatter said the congress's resolutions had given him "the instruments needed to restart the credibility of Fifa".
He also spoke of the need to make amends for all the negative publicity the organisation had generated.
"From the beginning I wanted this congress to know and understand we are in a situation which needs not only words but action in order to counteract all these attacks."
Blatter conceded the decision to have the bidding processes for two World Cups at the same time had been "a mistake" but said the move to have congress delegates vote on future World Cups was a step forward as it gave more power to individual football associations.
"I'm happy with this - it reinforces Fifa's pyramid, it will no longer be shaking."
The two-day congress in Zurich has seen plenty of public disputes and generated negative publicity for Fifa, but Blatter said it had ended with real achievement.
"We are very happy we have come to the unity of Fifa - at the beginning of congress we had doubts unity could be maintained," he said.
"Everyone was waiting for solutions - now we will apply them."
Earlier in the day, the chairman of England's FA, David Bernstein, had put a proposal to congress to delay the vote but 172 of 206 voters opted against a delay.
Blatter was unopposed because his rival Mohamed Bin Hammam, president of the Asian Football Federation, pulled out after being suspended over bribery allegations.
The English and Scottish FAs needed three-quarters of Fifa's congress to back their proposal but received little support, with Wales and Northern Ireland both choosing not to back a delay.
In an address to Fifa's congress on Wednesday, Bernstein asked for a delay "to allow time for an additional candidate or candidates to stand and compete in an open and fair election".
He added: "Only by doing so will the winner have proper credibility over the next four years."
The conclusion to his speech received a noticeably cool reception from the Fifa members in Zurich, with one or two applauding but the rest sitting in silence.
The lack of support became even clearer when several Fifa members who followed Bernstein to the
"Fifa belongs to 208 national associations and not to one association, we must not seek solutions through the media or a Parliament in any third country."
Representatives of Haiti, Benin, Fiji and Cyprus also expressed their disapproval to more enthusiastic applause.
Fifa senior vice-president Julio Grondona, also president of the Argentina FA, delivered a stinging riposte to his English counterparts.
"We always have attacks from England which are mostly lies with the support of journalism which is more busy lying than telling the truth," said the Argentine. "This upsets and disturbs the Fifa family.
"After hearing the speech from Sepp Blatter, we believe the calls we have made for greater transparency and better governance have been worthwhile," said Bernstein.
"While we did not succeed in deferring the presidential election, it was positive to be joined by 16 other nations in supporting our democratic request for the vote to be delayed, while a further 17 nations abstaining clearly shows that we are not alone or isolated in our views in relation to the current situation Fifa finds itself in. "
The FA had announced before the congress that it would be abstaining from the presidential vote and, even though their actions unsettled many Fifa members, they did receive the backing of the UK government.
"We agree with the FA that Fifa should have suspended the presidential election until the investigations had been completed," said a spokesman for Downing Street.
"The most important thing is for the public to have confidence in Fifa and for that to happen we need to have Fifa reform."
Blatter, who has held his post since 1998, has promised to implement changes at Fifa in the wake of the allegations of corruption as he told the congress he was determined to guide the organisation out of its current troubles.
"We have been hit and I personally have been slapped," said the Swiss, who continues to receive plenty of support despite the controversy which has surrounded Fifa.
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"I am the captain weathering the storm, this is a difficult period for Fifa and I admit that readily. Not only is the pyramid shaking but our ship has drawn some water.
"We need someone who will accept this responsibility. I'm willing to do this. And reforms will be made not just touch-ups but radical decisions, the necessary reforms.
"We must do something because I do not want ever again that we face this undignified situation."
Original presidential candidate Bin Hammam, along with Concacaf president Jack Warner, was provisionally suspended by Fifa's ethics committee over allegations that financial incentives were offered to Caribbean Football Union (CFU) members. Both have denied any wrongdoing.
Bin Hammam has appealed against his ban but was denied entry into the Fifa congress meeting on Wednesday.The controversy over his withdrawal resulted in the English and Scottish FA's action, with allegations of bribery concerning the World Cup bidding process also undermining Fifa.
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