Labor says the changes will entrench a Coalition majority, but the Government argues they reflect voter intentions more accurately.
There were heated exchanges overnight as the debate continued nonstop until its conclusion early this afternoon.
They were warned it would be a long night.
Special Minister of State Mathias Cormann said he was determined to push through the Government's legislation on changes to the system of voting for the Senate.
"If you still want to be here on Easter Friday, on Good Friday, that's fine."
Labor's Sam Dastyari made it clear he did not want it to go on that long.
"I'm not purporting this go for that long ... if for no other reason than -- it is true -- I do have tickets to Madonna on Sunday night in Sydney."
There were theatrics, too, with Independent senator Nick Xenophon wearing his pyjamas briefly in the upper house -- to make a point, he says.
Mr Xenophon, along with the Greens, had given the Government his support for the changes.
At one point, Labor senator Doug Cameron compared the Greens to characters from a Monty Python film, quoting from a famous film as he showed disdain for their support for change.
"They go, 'You empty-headed animal-food-trough wiper.' It says, 'I fart in your general direction.'* That's basically what he's done, and that's basically what they've done to you guys."
Labor has been accused of filibustering on the voting changes.
In the early hours of the morning, Labor senator Deb O'Neill even lectured on the meaning of the word filibuster.
"The word filibuster -- I'm indebted to Campbell Rhodes, of the Museum of Australian Democracy at Old Parliament House for his research here -- comes from the Spanish word, which is filibustero, which itself is derived from a Dutch word by the name of vrijbuite, which means 'pirate' or 'privateer.'"
The politicians sat through the night, with the Coalition and the Greens using their numbers to defeat a series of amendments.
As the debate neared its end, Opposition Senate leader Penny Wong criticised the Government for its failure to have a proper process in what she calls the biggest change in three decades.
"Their most urgent bill on the eve of an election is not about helping Australians but about helping themselves. It is not about jobs for Australians, it is about jobs for Coalition senators and Greens senators. Mr President, the Senate has just spent a day and night and a part of the day debating the Coalition-Greens deal on Senate voting, a timetable forced on it by a Government and a prime minister determined to get the keys it needs for a double dissolution and a Greens leader and party that's happy to oblige."
The passing of the bill -- after almost 40 hours of debate on it in total -- now means the Government could go to a double-dissolution election early and vote for an entirely new Senate.
Liberal Democrat senator David Leyonhjelm says he is sorry small minor parties just starting out will suffer.
Standing alongside Family First senator Bob Day, he says the fightback starts now.
"I'm here today with my mate Bob to urge everyone who is disgusted by all of this to get behind the minor parties. At the last election, one in four people voted for a party other than the major parties in the Senate. Most of these voters will vote for us again. Many more people have now seen the true colours of the professional politicians and the major parties, who exist only to accumulate power."
But Greens leader Richard Di Natale says it is a great outcome.
"We are of the view, as was the Government, that it's critical that, in a democracy, it's voters, rather than the backroom-preference operators, who are the ones who determine who gets elected."
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