Eric Hollingsworth defied his bosses and released a statement to the media on Wednesday condemning Pearson's decision to miss a pre-tournament training camp with her team mates in Glasgow in favour of racing in London.
He also said the athlete, who won gold at the London 2012 Olympic Games, had not told the truth about the support she had received from the Australian team.
Hours after releasing his statement, Athletics Australia announced Hollingsworth's suspension, expressing disappointment at the timing of his comments, insisting he should be focusing on supporting the athletes instead.
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"He acted without the authority of Athletics Australia and in contravention of the specific instructions of the Chief Executive Officer," Athletics Australia President David Grace said in a statement.
"Athletics Australia condemns in the strongest terms his disparaging comments about Sally Pearson and his timing.
"We have therefore suspended Eric Hollingsworth as an employee of Athletics Australia until such time as the Athletics Australia Board can convene to consider the matter.
"Action in regards to Eric Hollingsworth's role on the Commonwealth Games Team will be determined by the Australian Commonwealth Games Association, as the body responsible for the team."
Earlier, Hollingsworth, a former Britain decathlete, accused Pearson of a lack of professionalism ahead of the Games.
"Sally was coming along until the last minute, when she opted to take a race in London," he said in a statement released via an independent public relations agency.
"What's lost here is that she's the team captain and there's a reasonable expectation she'd be in the camp ahead of something as major as the Commonwealth Games.
"Her no-show sets a bad example to the entire national team."
There has been tension between the pair since Hollingsworth was critical of Pearson's second-place finish in the 60m hurdles at the world indoor championships in Poland in March.
It was the second time in less than 12 months that the 27-year-old had failed to successfully defend a world title, following another silver medal at the 2013 world championships in Moscow.
"I asked legitimate questions of her after the race, and she didn't like the line I was taking," Hollingsworth said.
"So via her agent she sought a meeting with Athletics Australia's president, CEO and high performance director, which I was not aware of until the day of, or day before, the meeting.
"While I thought at the time it was curious that I wasn't involved in that process in any form, Sally raised her issues, and the powers that be found no problems with my actions, and there was no case to answer.
"Subsequently Sally dug her heels in, as is her right, and asked for what is a new 'athlete performance advisor', which is the conduit between the athletes and Athletics Australia.
"I am that person for the bulk of the high-performance athletes, but not all, from a workload point of view. So we re-assigned Sally, which is fine. We had a good working relationship for nearly a decade, but she decided my challenging style wasn't what she was looking for, which is her prerogative."
Pearson has previously been critical of the Australia set-up, claiming she had not been provided with the medical support she required, but vowed to put her criticisms to one side while she concentrated on the Games in Glasgow.
"We've had a team physio travelling with Sally for the past three months, following her around Europe," Hollingsworth said.
"Since May we've provided this service, and there may have been one day or so where there's been an overlap when we've changed over personnel.
"To say we've withdrawn support is factually incorrect and a little disappointing."
Hollingsworth's role with the team during Glasgow 2014 is now unclear, with the Australian Commonwealth Games Association yet to make public their decision.
Pearson begins the defence of the title she won at Delhi 2010 on Thursday.
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