The vote came after the opposition seized several official buildings in the capital Kiev and parliament appointed high-level officials.
Viktor Yanukovych described events as a “coup” and vowed not to stand down.
Also on Saturday afternoon, prominent opposition leader Yulia Tymoshenko was released from detention, hours after parliament authorized the move.
Correspondents say Yulia Tymoshenko was driven away in a car after leaving a hospital in the eastern city of Kharkiv where she was being held under prison guard.
Yulia Tymoshenko is now reported to be heading to Kiev’s Independence Square – also called the Maidan – which has been the focal point of anti-government protests.
Lawmakers had voted to pave the way for Yulia Tymoshenko’s release on Friday. She was sentenced to seven years in prison in 2011 after being convicted of abuse of power over her actions during her tenure as prime minister.
Yulia Tymoshenko’s supporters have always maintained this was simply Viktor Yanukovych taking out his most prominent opponent, and her release has always been a key demand of the protest movement.
The opposition is now in effective control of the capital Kiev, with Viktor Yanukovych arriving in Kharkiv, near the Russian border, late on Friday night.
The Interfax news agency reported parliament speaker Oleksandr Turchynov as saying Viktor Yanukovych had been stopped by border police in an attempt to flee to Russia and was now somewhere in the Donetsk region.
Earlier on Saturday, protesters walked unchallenged into the president’s office and residential compounds.
Ukraine’s army released a statement on Saturday afternoon saying it would not get “involved in the domestic political conflict”.
The vote to “remove Viktor Yanukovych from the post of president of Ukraine” was passed by 328 MPs.
Such ballots, passed by what is called constitutional majority, are binding and enter into force with immediate effect.
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