The vote on the Labor and Greens motion was held on August 13, with 37 in favour and 27 against.
The Abbott government had earlier refused a Senate motion ordering it to table further documents detailing the $1.6 billion project's costs and benefits.
Senator Scott Ludlam and Senator Glenn Sterle are particularly curious about the decision-making process that led to it receiving federal government funding.
The Perth Freight Link is the largest road project to be undertaken in Western Australia, with $925 million coming from the Commonwealth and a commitment of $650 million from the state government.
It will also be the state's first toll road, but only trucks will be charged.
The aim is to divert hundreds of trucks a day from Leach Highway, which runs through several residential suburbs, and provide a direct freight route from Muchea in Perth's north to Fremantle Port.
A wide range of groups are opposed to it, including residents who have been warned they could have their property resumed.
Others are concerned a key component of the project, the Roe Highway extension or "Roe 8", will cut through the Beeliar wetlands, home to the endangered Carnaby's black cockatoo.
In the WA parliament on Thursday, Transport Minister Dean Nalder defended the plan robustly, but not quite as vehemently as Premier Colin Barnett.
"You can go up there like your mate Scott Ludlam in Canberra and you can argue against a link between Roe 8 and Fremantle - you will strangle the port and you will strangle Fremantle," Mr Barnett told the opposition.
While WA Labor leader Mark McGowan questioned why Mr Nalder was set on signing up contractors by November "even though you have not determined a route", Mr Nalder said swift action was needed because traffic flowing to and from the port was going to rapidly surge.
"We have a critical time period coming up, a critical junction when the proponents come back to us with possible solutions," Mr Nalder said.
"Now at that point, we may move away from the base case and therefore we may need to look at the timing."