The mayor said it was “the right thing for TfL to have done” and that the organisation now needed to follow its processes on whether the driver should face disciplinary action.
Footage posted online apparently showed the chant being led over the train’s speaker system on Saturday, as about 100,000 protesters took part in a pro-Palestinian demonstration.
The words "free, free" could be heard and passengers responded "Palestine" - a popular chant at protests.
Mr Khan confirmed to the Standard that he had not personally played any role in ensuring the driver’s suspension.
He said: “It’s really important, even though I’m the chair of TfL, that I stay out of individual cases, for obvious reasons - it could prejudice the outcome. What I don’t want to do is, because of me, the process being challenged as unfair.
“But the commissioner [of TfL, Andy Lord] reassured me on Saturday that the processes were going to be followed. He made sure that steps were taken to identify the line, the train, the driver.”
Met Police commissioner Sir Mark Rowley has meanwhile said that hate crime laws "probably need redrawing" as he faced questions about the policing of Saturday’s pro-Palestinian rally.
A video posted online appeared to show a man shouting "jihad" at a separate event from the main march. Having reviewed the clip, the Met said they had not identified any offences.
Sir Mark said police were "ruthless in tackling anybody who puts their foot over the legal line".
But he added: "Our job is to enforce to that line, Parliament's job is to draw that line - maybe some of the lines aren't in the right place."
Downing Street said there were "no plans" to give police more powers to deal with chants deemed to be extremist. Sir Mark said he had discussed the matter with Home Secretary Suella Braverman.
Mr Khan said he supported Sir Mark in raising the issue.
“The job of the police is to enforce the law,” he said. “They can’t apply the law with their own inherent prejudices, which we all have. They’ve got to apply the law without fear or favour.
“What the police are also doing is working with lawyers from the Crown Prosecution Service, if there’s any confusion about what the law is.
“Over the course of this weekend and last weekend, by and large, the vast majority of protesters protested in a way that was lawful, peaceful and safe.
“I’m afraid a small minority appear to have broken the law. There have been more than 30 arrests - there may be more arrests coming around the corner.”
He added: “If it’s the case that Parliament is unhappy with the current law, they can change the law.”