The much-delayed election kickstarts a political process which should also see lawmakers agree on a federal president, who then designates the largest bloc, the candidate of which has the first chance to form a government.
When it is eventually formed, the new government will face the daunting task of steering the country through its worst crisis in years.
Juburi won 194 out of the 273 votes cast, with most of the rest deemed invalid and only 19 going to his only rival, an obscure candidate elected to parliament on a secular list.
Lawmakers remained in the chamber after the vote to elect two deputy speakers, AFP reported.
The speaker presides over an institution that has consistently failed to fulfil its duties and whose powers are dwarfed by those of the prime minister.
Some in Prime Minister Nouri al-Maliki's alliance have said that the voting would only go ahead once a comprehensive deal was struck between the main blocs on the three presidencies, but it was unclear if that has occurred.