Shavkat Mirziyoyev garnered 88.61 per cent of the vote, Central Election Commission head Murza-Ulugbek Abdusalomov said during a briefing in Tashkent. Turnout was 87.83 per cent, according to officials.
None of the other three presidential contenders managed to get more than 4 per cent of the ballots cast.
While there were some minor improvements compared to previous elections, the vote was marred by a muzzled media, lack of independent candidates and widespread falsification, according to a report released by the Organization for Security and Cooperation in Europe's Office for Democratic Institutions and Human Rights.
But the result will consolidate Mirziyoyev's position following his appointment as acting president just six days after Karimov's death was announced at the beginning of September.
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Karimov led Uzbekistan since before the 1991 Soviet collapse, first as its communist boss and then as its president.
During his long tenure, he ruthlessly crushed all opposition and was denounced by international rights groups for abuses that included killings and torture. His death raised concerns that the predominantly Sunni Muslim nation of 32 million might see fierce infighting over the choice of a successor.
Russian President Vladimir Putin was one of the first world leaders to congratulate Mirziyoyev. In a phone call, Putin invited Mirziyoyev to visit Russia, the Kremlin said in a statement.
While Mirziyoyev is known as pro-Russia and is expected to move Uzbekistan closer to Moscow, he is also likely to make overtures to Europe and the West, according to Daniil Kislov, the editor of Moscow-based news agency Ferghana.Ru.