Mr Khan questioned why the two women assumed that "members of the British Jewish community support every action of the Israeli government?”
In response, they claimed that "these Israeli Zionists” were trying to destabilise Labour and undermine Jeremy Corbyn.
Journalist and JC columnist Jonathan Freedland, who witnessed the incident, revealed on Twitter that he "fought the urge" to explain that JLM was Labour's oldest affiliate and had deep roots in the British Jewish community.
Or that JVL was set up to deny allegations of antisemitism in Labour and represents a tiny fringe of British Jewish opinion.
Mr Freedland said Mr Khan turned his back on the pair to end the conversation.
He later tweeted: "What I saw was the leader of our capital city and a proud Muslim stand with his Jewish ‘brothers and sisters’ against those who would exclude Jews. It was both depressing and heartening.
"We Jews know we have enemies - but we also have friends."
On Monday night a fringe event by the Labour Representation Committee went ahead at Brighton's Rialto Theatre, with suspended MP Chris Williamson and Jackie Walker, who was expelled from the party earlier in the year, among the speakers.
Film director Ken Loach also attended the event, where cartoons about Benjamin Netanyahu by Steve Bell, which the Guardian refused to publish, were auctioned in a raffle.
Also present at the LRC event was Jeremy Corbyn’s wife, Laura Alvarez.
Shadow chancellor John Mcdonnell, who is honorary president of the group, did not attend.
Earlier, Waterstones cancelled the launch of a book on media coverage of the Labour antisemitism row at its Brighton shop.
The book, Bad News for Labour Antisemitism, the Party and Public Belief , contains chapters critical of the International Holocaust Remembrance Alliance definition of antisemitism.
Waterstones’ managing director James Daunt cited concerns about how the event was being planned.
