Nouri al-Maliki, Iraq's incumbent prime minister, demanded the recount and alleged fraud had occurred after provisional results handed a two-seat lead to the political bloc led by his rival, Iyad Allawi.
Baghdad province accounts for about a fifth of parliament's 325 seats. Al-Maliki had challenged results in four other provinces as well, but those requests were denied.
The recount was carried out inside the green zone under the supervision of observers from the UN and the European Union.
Iraq's parliamentary polls produced no clear winner, with Allawi's Iraqiya coalition winning 91 seats, and al-Maliki's State of Law bloc coming a close second, with 89 seats.
A political bloc needs 163 seats in parliament in order to form a government.
The Iraqi National Alliance (INA), a coalition led by Shia religious groups, had finished third with 70 seats.