The political opposition had insisted that Gul was not truly committed to Turkey's secular system, boycotting two sessions of parliament in April and May.
The boycott prevented the house from having the necessary quorum required to hold a presidential vote.
As tensions increased over Gul's candidacy, the army warned that it was set to defend the secular order, and mass anti-government demonstrations were held across Turkey.
Recep Tayyip Erdogan, Turkey's prime minister, called early general elections on July 22, in which the AKP won a landslide victory.
The new parliament, which due to open on Saturday, is expected to elect a successor to Sezer by the end of August.
Sezer has remained acting head of state since his seven-year term expired in May.
The government had planned to hold the referendum simultaneously with the July 22 elections, but legal issues delayed the approval of the package.
The constitutional amendments also call for a once-renewable, five-year presidential mandate instead of a single, seven-year term, and general elections every four years instead of five.