The upper house chamber was meant to have adjourned on Thursday for six weeks, but an extra day was scheduled.
Communications Minister Stephen Conroy threw parliament into disarray by springing forward 35 amendments to an access arrangements bill.
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The process was slow, and threatened to spill over into Saturday.
Shortly after 9.30pm AEDT, however, the Senate voted 34 to 32 to pass two key NBN bills, with the Australian Greens and crossbench senators Nick Xenophon and Steve Fielding siding with Labor.
After a 12-hour sitting, senators voted on 23 pages of amendments governing the commercial operations of the company behind the $36 billion project.
Earlier in the evening, the government compromised on its most contentious amendment, covering the role of the competition regulator.
The minister originally wanted the Australian Competition and Consumer Commission (ACCC) to get permission from NBN Co to vary any points of interconnect.
But Senator Xenophon and the Greens jointly put forward their own amendment so NBN Co would not have a right of veto over an ACCC decision.
It passed 34 to 32, with the government siding with crossbench senators.
The amendment also called on the ACCC to review by June 2013 policies relating to network interconnection points.
The coalition supported the crossbenchers' amendment, but ended up voting against the government's entire amendment with the changes.
Still, the NBN Companies bill and an access arrangements bill have both passed the Senate.
In a statement, Senator Conroy said the passage of amendments covering national wholesale pricing would translate into affordable retail prices for high-speed broadband "for all Australians no matter where they live".
"Passage of these bills further underpins the Gillard government's policy to deliver structural reform of the telecommunications industry to promote, for the first time, sustainable retail-level competition," he said.
His media release failed to mention how earlier in the day, the minister took issue with National Senate leader Barnaby Joyce's call for unit pricing regulations so satellite and wireless services in remote areas could be delivered at the same price as high-speed optical fibres in major cities.
Lower house MPs are now due back in Canberra on Monday to consider the bills.
Opposition communications spokesman Malcolm Turnbull said Senator Conroy created an enormous legislative challenge with his rush of amendments.
"This is a big deal but the government is making it up as it goes along, it is chaotic, it is dysfunctional," he told ABC Television.
Australia's No 2 telco Optus earlier expressed concern about amendments being sprung at short notice.
When it came to Telstra, the biggest telco, the government insisted the amendments need to be resolved so there was no commercial uncertainty as it dealt with NBN Co.
The Senate was adjourned at 10pm AEDT, and is not scheduled to return until May 10 which is budget day.
