A vote shortly after 1.30pm on Friday ended nearly 40 hours of debate, making it one of the longest Senate considerations of a single bill in the past 26 years.
The government's legislation was supported by the Greens and independent South Australian senator Nick Xenophon.
Labor and other crossbenchers voted against the changes which will allow voters to allocate their own preferences above the line on the Senate ballot paper.
And if they choose to vote below the line they won't have to number every box - in some states that could be as many as 100.
As well group voting tickets will be abolished, a move crossbenchers fear will purge the Senate of micro-party senators.
Special Minister of State Mathias Cormann praised all senators, even those opposed to the changes, who made an active contribution to the debate.
"It's a reform which will help ensure that future Senate election results truly reflect the will of the Australian people," he said.
Opposition Senate leader Penny Wong wasn't nearly as effusive.
"It says everything about this government that their most urgent bill on the eve of an election is not - is not about helping Australians, but about helping themselves," she told parliament.
Senator Wong took a swipe at the Greens, telling the minor party its support for the changes risked giving the working majority in the upper house over time.
The bill which passed with nine government amendments needs to be approved by the lower houses.
MPs have been on standby for a recall of the house, expected within the hour.
The new laws will apply from July 1, allowing the government to use them for a double-dissolution election.
Marathon senate debates since 1990
- Howard government changes to native title laws in 1997: 106 hours.
- Introduction of the GST in 1998-99: 69 hours.
- Kevin Rudd's carbon emissions reduction scheme in 2009: 64 hours.
- The Keating government's Native Title Bill in 1993: 52 hours.
- Howard government's workplace relations changes in 1996: 48 hours.
- Labor government money bills in 1992: 40 hours.
- Changes to the way senators are elected in 2016: 40 hours.
- Research involving human embryos in 2002: 36 hours.
(Source: Australian Parliament website).
