A small group clutching masks of Ms Deeming's face and a sign labelling Mr Pesutto a "bully" shouted "shame, shame" as he took the stage at the party's state council in Bendigo on Saturday.
Mr Pesutto was heckled and dozens of Liberal members walked out as he kicked off the two-day event, with speculation rife that a leadership challenge is looming.
Tensions flared between members over the decision to expel Ms Deeming from the parliamentary team last week.
The members who walked out called for Mr Pesutto to be replaced as leader, The Age newspaper reported.
Mr Pesutto brushed off the incident.
"I was very moved by the two standing ovations that occurred during my speech at the start and at the end," he told reporters.
"If there are people who had different views, that's a matter for them but what I saw was a strong endorsement of my commitment to reforming the party, making sure that we're an effective opposition and then the government in 2026."
He said every political party has members with different views and he was focused on uniting them.
"My responsibility and my determination is to always bring those people together in a common cause even though they might have different views on things," he said.
Mr Pesutto discussed policy and the future of the party, which remains fractured after Ms Deeming was booted for bringing discredit to the Liberal brand.
Former federal Liberal candidate Warren Mundine was among those calling for Mr Pesutto to be replaced as the Victorian party leader.
"@JohnPesutto has divided and destroyed any chance of the Coalition returning to power at the next Vic State election. He must be replaced as leader! #istandwithMoiradeeming," Mr Mundine tweeted after the state council meeting.
Ms Deeming was condemned for attending an anti-transgender rights rally where neo-Nazis were present, but maintains she has no ties to them.
Liberal MPs voted 19 to 11 to expel her amid legal threats from Ms Deeming after Mr Pesutto refused to publicly declare she is not a Nazi sympathiser.
After attending the rally in March, Ms Deeming was suspended for nine months and an expulsion motion was brought to the party room last week after the MP served Mr Pesutto with a defamation concerns notice.
She now remains on the crossbench as an independent.
One of Ms Deeming's supporters Renee Heath was also removed from her role as parliamentary secretary.
Mr Pesutto said the Victorian Liberal Party needs to be broad and inclusive to win the next state election.
"In order to win, we need to get to 45 seats - I'd love to get to 56 seats which is what (Premier) Daniel Andrews has," he said.
"In order to do that, you need to appeal broadly and whether we like it or not that's what Labor's been able to do."
He vowed to reform the state's tax system, in his first major policy announcement.
The party disagreement over Ms Deeming has drawn criticism from Opposition Leader Peter Dutton who earlier this month said he was considering an intervention.
He said the controversy was damaging to the Liberal brand.
"The whole mess needs to be sorted out sooner rather than later," Mr Dutton previously told ABC Radio.
"The Liberal party should have been more competitive at the last state election. They weren't and they need to be a credible alternative government."
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