Protesters raised a large poster which depicted the Tunisian president pouring water on the bloodied hands of the Saudi crown prince - suggesting Tunisia's complicity in washing away guilt.
The two held talks on Tuesday before the king continued on to Tunisia.
Khashoggi's murder also put a spotlight into Saudi Arabia's war in Yemen, with United States lawmakers pushing the Trump administration to stop its support for the Kingdom as a punishment for the killing.
"We don't need your oil barrels, or your petro-dollars".
According to the UN, Yemen is the world's worst humanitarian crisis.
But he said that among the issues that had not been investigated under the Republican leadership of the House "is whether the Russians have been laundering money through the president's businesses and this is the financial hold that the Russians may have".
"We refuse to turn Tunisia into a destination to whitewash war crimes", she said.
"Tunisia is pure now".
Sarah Leah Whitson, HRW's Middle East and North Africa director, said the worldwide rights group took the case to Argentina because Prince Mohammed will attend the opening of the G20 summit this week in Buenos Aires.
The New York-based rights group said it had filed a submission with Argentine prosecutors calling on them to invoke the country's universal jurisdiction statute to prosecute the crown prince for alleged war crimes committed by the Saudi-led coalition in Yemen.
Meanwhile advocacy group Human Rights Watch (HRW) wrote to a federal prosecutor arguing that the Argentinian courts should prosecute the crown prince under Argentinian law when he arrives there later this week. Still, Argentine media cited judicial sources in recent days as saying it was extremely unlikely for Buenos Aires to take up the case against MBS.
The crown prince is on a tour of the region, one that won't include Morocco, after its king reportedly snubbed the Saudi leader. Fortunately we have a USA intelligence community that's really good at a lot of us in the first branch of government, the article one branch, the Congress, have heard from the intelligence community and I will be getting another classified briefing on Tuesday about this.
In a controversial move past year, Trump recognised Jerusalem as Israel's capital and later moved the USA embassy there. "And should Congress look into see if he's got financial motivations into why he might be siding with the Saudis over the Central Intelligence Agency?"
But Tunisians' anger towards Israel goes beyond a pro-Palestinian sentiment.
But many Tunisians are angry over the killing and suspicions of the prince's involvement.
Flags from several African countries could be seen in Tuesday's protest, most visibly those of Egypt and Algeria.
Almost 100 Egyptian journalists have announced their rejection of the visit of Saudi Crown Prince Mohammad bin Salman to Cairo.
"Universal jurisdiction cases are an increasingly important part of global efforts to hold those responsible for atrocities accountable, provide justice to victims who have nowhere else to turn, deter future crimes, and help ensure that countries do not become safe havens for human rights abusers", the statement highlighted.