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Mr Anastasiades and Mr Malas, backed by the left-wing Akel party, will now contest the run-off vote.
BBC: Cyprus election: Anastasiades and Malas go to run-off
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With all the votes counted, Mr Anastasiades, a conservative, secured 45.46%, well ahead of his nearest rival, Stavros Malas, on 26.91%.
BBC: Cyprus election: Anastasiades and Malas go to run-off
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According to the latest polls, his closest rival among the 10 other candidates is Mr Malas, who is backed by Akel, closely followed by Giorgos Lillikas, an independent.
BBC: Cyprus votes for new president amid economic crisis
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Mr Malas supported a bailout but opposed austerity.
BBC: Cyprus election: Nicos Anastasiades elected president