The Fair Work Commission has ordered companies in the sector to review their rates twice every month to account for the high costs of petrol and diesel.
The orders will come into effect from Tuesday and will be in place as long as the weekly average price of diesel is above $2 per litre.
The ruling followed a case submitted by the Transport Workers' Union to the workplace watchdog.
Secretary Michael Kaine said the decision was historic.
"(The order) for the first time, puts obligations on the wealthy clients at the top of our supply chains to pay their fair share to the transport industry," he said.
"Over the last few weeks drivers and transport businesses have outlined the dire circumstances they are facing with diesel costs, many already having to park up their trucks or rely on personal loans just to keep going."
The decision comes as the owners of the Geelong Viva refinery, which was damaged in a fire on Wednesday night, said the site was expected to return to almost full capacity in the coming weeks.
In a statement to the ASX, Viva Energy said capacity was set to ramp up at the facility.
"Over the next few weeks, and subject to plant inspection, the company expects to be in a position to ... lift production of diesel, jet fuel and petrol to over 90 per cent of capacity," the statement said.
"The refinery is then expected to continue production at these levels until repairs are completed."
The refinery was at 60 per cent output for petrol following the fire and at 80 per cent for jet fuel and diesel.
Viva has promised a full investigation into the cause of the incident.
The company had been in a trading halt following the fire, but selling resumed on Monday morning.
Viva shares dropped by as much as 9.5 per cent when it came out of the halt and were sitting at $2.34 by mid-afternoon, down about 7.7 per cent.
The Geelong facility is one of only two refineries operating in Australia and provides 10 per cent of the country's fuel supply and 50 per cent of Victoria's.
Production had been increased at the refinery following the closure of the Strait of Hormuz, which placed pressure on global oil supply.
Freight and trucking firms from Monday were also able to apply for interest-free loans to help weather the price hikes of doing business.
The loans were part of a $1 billion economic resilience program package and will apply to businesses that make or transport fuels, fertiliser and agricultural products.
The concessions were announced by Prime Minister Anthony Albanese during a speech at the National Press Club earlier in April.
Industry Minister Tim Ayres said the loans would provide stability during volatile economic times.
"The billion dollar facility is there to be used as much as it is required," he told reporters in Canberra.
Loans of up to $5 million are available for companies with a turnover less than $100 million.
Australian Banking Association chief executive Simon Birmingham said the financial sector would support the rollout of the loans.
"Banks are stepping up to support the rollout of these zero-interest loans to businesses who are doing it tough as a result of the current conflict in the Middle East," he said.
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