The four-day visit has been marred by ongoing protests and hostility across multiple states after the president was invited by Prime Minister Anthony Albanese's government following the Bondi terror attack.
Both leaders have largely praised the visit, describing it as an opportunity to strengthen relations and advance discussions about the Middle East.
Leading human rights expert Ben Saul told AAP he believed the visit had deepened divisions within both countries, taking aim at the president's attitude ahead of his arrival.
"He didn't come solely on a mission to mourn the victims of Bondi. He made it clear before he got on the plane," Professor Saul, who is a United Nations special rapporteur on human rights and counterterrorism, said.
"It hasn't been about the victims of Bondi, it's been a deliberate political visit."
During his visit in Sydney, he met victims of the Bondi terrorist attack, students from Jewish schools and attended a ceremony at the Chabad of Bondi with Mr Albanese.
He travelled to Canberra before making his way to Melbourne.
Each stop triggered various levels of protests by groups who opposed Mr Herzog setting foot on Australian soil, calling for federal police to investigate the Israeli president for alleged war crimes.
At least nine people were charged and 27 arrested after police punched and pushed protesters during an anti-Herzog rally in Sydney, while upwards of 10,000 people attended the Melbourne rally.
Protesters have been calling for Mr Herzog's arrest, despite the president being granted customary immunity under international law as a visiting head of state.
Israeli Prime Minister Benjamin Netanyahu is subject to an International Criminal Court arrest warrant, but Mr Herzog is not.
A UN Special Commission of Inquiry found comments made by Mr Herzog following the Hamas terror attack in Israel on October 7, 2023, had been reasonably interpreted as incitement for genocide.
Israel has repeatedly denied allegations of genocide and Mr Herzog subsequently clarified his remarks, which he said were taken out of context.
Professor Saul believes the relationship between the two nations cannot be repaired until Israel investigates the allegations of war crimes.
"Given the severity of Israel's violations, this isn't the time to soft pedal," he said.Â
"Australia says it cares about the international legal order, well you have to speak up for them because, in this age, there aren't many countries doing that."
Mr Albanese said after meeting the Israeli president on Wednesday that Australia wanted Israelis and Palestinians to live side by side in peace and security.
During his meeting, he had raised the death of Australian aid worker Zomi Frankcom, who was killed by an Israeli drone strike while working for World Central Kitchen in April 2024.
"We have made it clear that remains the Australian government's position and we've also made clear our expectation that there be transparency about Israel's ongoing investigation into the incident," Mr Albanese said.
"We continue to press for full accountability, including any appropriate criminal charges."
Members of the Jewish community welcomed the visit, with Australian Jewry Executive Council's Alex Ryvchin calling it a tremendous moment.
He believed the face-to-face meetings with leaders, including Mr Albanese had helped strengthen the relationship between both countries.
"We've seen since October 7, a deterioration in relations between the two countries, which have always been historically strong," Mr Ryvchin told AAP.
"It's a lot easier to kind of send aggressive tweets or issue public statements condemning the other side when you don't see them and when they're distant. But when the president gets to sit across from our leaders, it humanises each other.
"It helps to build a strong, constructive relationship going forward."
Despite the tension over the past four days, Mr Herzog expressed he had brought a message of goodwill to Australia and was using his visit to strengthen and console the Jewish community.
"We came here to be with you, to look you in the eye, to embrace and remember," he said on Thursday.
"We return to Israel feeling empowered."
Mr Herzog departed Melbourne on Thursday night, concluding his visit.
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