Independent senators Rex Patrick and Stirling Griff both lost their seats at the expense of the Greens' Barbara Pocock and the Liberals' Kerrynne Liddle.
The Australian Electoral Commission has listed the Liberals with three seats, Labor with two and the Greens with one, after six of the state's 12 Senate spots were up for election.
Former finance minister Simon Birmingham was re-elected on the top of the Liberal ticket, while the new Foreign Affairs Minister Penny Wong topped Labor's.
Liberal senator Andrew McLachlan and Labor senator Don Farrell - who has been sworn in as the new trade and tourism minister - were also re-elected.
The tally of the Senate's 76 seats currently sits at 32 to the coalition, 26 to Labor, 12 to the Greens, two to both One Nation and the Jacqui Lambie Network and one to independent David Pocock, according to the ABC's predictions.
The final Victorian Senate spot remains too close to call, with the United Australia Party's Ralph Babet ahead of incumbent Liberal senator Greg Mirabella, who was only sworn in in February after filling a casual vacancy.
Tasmania's Senate race result will be declared on Thursday.
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