The judgment, handed down by the Court of Appeal in Melbourne on Thursday, means the Pitch Perfect actress will receive about $3.9 million less than she had originally been awarded.
The articles falsely claimed she lied about her real name, age and childhood in a bid to make it in Hollywood.
However the Court of Appeal found "there was no basis in the evidence for making any award of damages for economic loss".
Wilson was not in court for the ruling in Melbourne this morning.
In September past year, Wilson won the largest defamation payout in Australian legal history, with Bauer ordered to pay $4.56 million in damages after accusing Wilson of being a serial liar in one of their magazines.
"In the lead up to today, major media organisations united in an unprecedented way to support Bauer's appeal in relation to that issue".
She took to social media on Wednesday night to say regardless of the outcome she had "already won the case".
The $650,000 compensation was also reduced to $600,000.
Australian actress Rebel Wilson speaks to the media out the front of the Victorian Supreme Court after a jury of six has returned unanimous verdicts in favour of Wilson against Bauer Media.
It was the biggest defamation payout in Australian legal history.
When Wilson won the case previous year, it was an Australian record for a case, much higher than the AUS$389,000 maximum previously set, by using her "global reach" as justification.
Wilson argued the "serial liar" allegations had ruined her reputation and cost her lucrative movie roles.