Federal Court Justice Michael Lee on Thursday ordered Mr Palmer to cover the costs of the WA premier's cross-claim from December 22 last year, around when the billionaire had rejected his rival's offer to settle the proceedings.
He ordered that both parties cover their own expenses incurred prior to that date.
Mr McGowan, whose trial barrister Bret Walker SC is reported to charge up to $25,000 per day, on Thursday told parliament he didn't know the full amount but there would be some cost to taxpayers.
Justice Lee last week found Mr Palmer and Mr McGowan had defamed each other in 2020, when they feuded over Western Australia's COVID-19 response and a damages claim involving one of Mr Palmer's mining projects.
He ordered Mr Palmer to pay $20,000 to Mr McGowan, who was in turn directed to pay $5000 to the Queensland businessman.
In a letter sent to Mr Palmer's lawyers last December, Mr McGowan's legal team proposed discontinuing the proceedings with both sides bearing their own costs.
Mr Palmer did not respond to the proposal, the court heard.
Justice Lee said the billionaire had been obliged to resolve the proceedings as quickly as possible, having launched them in the first place.
"The notion that Mr Palmer and Mr McGowan are equally responsible for these proceedings having consumed significant private and public resources cannot be reconciled with the objective facts," the judge said.
"Both men went too far in their political jousting, and both men litigated, but only one was willing to draw back and avoid a long and costly hearing."
It should have been evident in December that the cost of the litigation was "disproportionate to any benefit it was likely to produce", Justice Lee added.
Mr Palmer's lawyer Barry Dean earlier said the offer had been made late in proceedings and would have deprived his client of the court's vindication.
"The main point is that ultimately my client did succeed on his claim," Mr Dean told the court.
Mr Palmer had sought up to $30 billion in damages over a 2012 decision by the former Liberal state government not to assess his proposed Balmoral South iron ore project.
The McGowan government in 2020 rushed through extraordinary legislation to block the claim.
Speaking under parliamentary privilege on Thursday, Mr McGowan claimed Mr Palmer had sought to "force his hand" through the defamation lawsuit.
"His real frustration was my government's legislation that stopped him taking us for $30 billion," the premier said.
"I believe his real motivation was to get billions of dollars from taxpayers ... by the construct of suing me for defamation."
The premier added that the $20,000 in damages he had been awarded would be returned to state coffers.
Justice Lee last week found Mr McGowan's insults against Mr Palmer - including labelling him an "enemy of the state" - were not trivial but ultimately caused very little damage to his reputation.
Mr Palmer's attacks on Mr McGowan had probably only enhanced the premier's reputation and popularity within his home state, the judge said.
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