The 65-year-old singer clashed with the 57-year-old guitarist during the band's gig in Boston with the group subsequently cancelling the remainder of their North American tour dates.
Perry has since apologised in a statement on his Instagram Story.
"This weekend has been incredibly difficult and after having the time and space to reflect, it is only that I apologise to my bandmates, especially Dave Navarro, fans, family and friends for my actions during Friday's show," he wrote.
"Unfortunately, my breaking point resulted in inexcusable behaviour, and I take full accountability for how I chose to handle the situation."
Earlier on Monday, the band announced they had decided to scrap the rest of their tour, with a statement posted on Navarro's Instagram account, signed by the guitarist and his bandmates Eric Avery and Stephen Merkins.
View this post on Instagram A post shared by Dave Navarro (@davenavarro)
"Due to a continuing pattern of behaviour and the mental health difficulties of our singer Perry Farrell, we have come to the conclusion that we have no choice but to discontinue the current US tour," the statement said.
"Our concern for his personal health and safety as well as our own has left us no alternative. We hope that he will find the help he needs."
The band are broken-hearted about the situation - but insisted they have no realistic alternative.
"We deeply regret that we are not able to come through for all our fans who have already bought tickets.
"We can see no solution that would either ensure a safe environment on stage or reliably allow us to deliver a great performance on a nightly basis.
"Our hearts are broken. Dave, Eric and Stephen."
The band were scheduled to play another 12 concerts across the US and Canada in coming weeks.
Jane's Addiction is known for edgy, punk-inspired hits Jane Says, Been Caught Stealing and Just Because in the late 1980s and early 1990s as the alternative rock and grunge music movements were growing. It has three top five hits on Billboard's Alternative Airplay chart.
With AP
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