Joyce's victory gives the ruling conservative coalition exactly half the seats in the House of Representatives.
Parties need a majority in the House to govern without making deals with independent lawmakers.
Joyce is one of nine lawmakers who lost their jobs for contravening a unique Australian constitutional quirk that demands lawmakers must be solely Australian citizens.
He was among five lawmakers the High Court disqualified from Parliament in October. The court rejected the government's argument that Australians unaware that they had inherited another nationality from a parent should be exempt from the constitutional ban.
But Joyce was able to stand for re-election because he has renounced the citizenship he had inherited from his New Zealand father.
Turnbull's weak control of the Parliament showed on Thursday when he was forced to announce an inquiry into corruption in the banking industry. He had argued against such an inquiry for almost two years, but government lawmakers were threatening to band with opposition lawmakers to force it to happen.
The government has mostly trailed the center-left opposition in opinion polls since it was re-elected for another three-year term last year.
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