(Julian Assange had been cited as saying the release of the allegations was "deeply disturbing")
The Swedish Prosecution Authority website said the chief prosecutor had come to the decision that Mr Assange was not suspected of rape but did not give any further explanation.
The warrant was issued late on Friday.
Wikileaks, which has been criticised for leaking Afghan war documents, had quoted Mr Assange as saying the charges were "without basis".
That message, which appeared on Twitter and was attributed directly to Mr Assange, said the appearance of the allegations "at this moment is deeply disturbing".
In a series of other messages posted on the Wikileaks Twitter feed, the whistle-blowing website said: "No-one here has been contacted by Swedish police", and that it had been warned to expect "dirty tricks".
In its "official blog" on Saturday before the warrant was cancelled, Wikileaks said it was "deeply concerned about the seriousness of these allegations. We the people behind Wikileaks think highly of Julian and and he has our full support".
The current whereabouts of Mr Assange, a 39-year-old Australian, are unclear.
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The Swedish Prosecution Authority website said chief prosecutor Eva Finne had come to the decision that Julian Assange was not subject to arrest.
In a brief statement Eva Finne said: "I don't think there is reason to suspect that he has committed rape."
The website said there would be no further immediate comment.
Earlier, Karin Rosander, communications head at Sweden's prosecutors' office, said there were two separate allegations against Mr Assange, one of rape and the other of molestation. She gave no details of the accusations. She said that as far as she knew they related to alleged incidents that took place in Sweden.
On Saturday she said the police investigation into the molestation charge continued.
Ms Rosander said: "The [chief prosecutor] will look into that later. She hasn't been able to do that, but that's not enough for being arrested. It's not a serious enough crime."
Media reports say Mr Assange was in Sweden last week to talk about his work and defend the decision by Wikileaks to publish the Afghan war logs.
Last month, Wikileaks published more than 75,000 secret US military documents on the war in Afghanistan.
US authorities criticised the leak, saying it could put the lives of coalition soldiers and Afghans, especially informers, at risk.
Mr Assange has said that Wikileaks is intending to release a further 15,000 documents in the coming weeks.
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