However, Mr Trump Jr neglected to mention that Mr Khan was noting that residents need to "be prepared" for such attacks.
Mr Khan chose not to respond to the 39-year-old New Yorker's comments directly, telling CNN: "I'm not going to respond to a tweet from Donald Trump Jr. I've been doing far more important things over the last 24 hours."
Mr Trump Jr's tweet included a link to a September 22 story from Britain's Independent newspaper that included Mr Khan's quote to the Evening Standard days earlier.
Mr Khan was speaking to the newspaper from New York, a day after a bomb went off in the city, leaving more than two dozen people hurt.
"Part and parcel of living in a great global city is you've got to be prepared for these things. You've got to be vigilant. You've got to support the police doing an incredibly hard job," he had said.
Mr Trump Jr was widely criticised for the tweet, with British Member of Parliament Wes Streeting calling him a "a disgrace" and accusing him of using a terrorist attack for "political gain."
It comes as President Donald Trump tweeted his condolences to the American killed in the London attack.
Kurt Cochran, 54, was touring Europe with his 46-year-old wife, Melissa, when they were mowed down by the terrorist on the south end of Westminster Bridge. Mr Cochran died from his injuries, while his wife is recovering in hospital.
"A great American, Kurt Cochran, was killed in the London terror attack. My prayers and condolences are with his family and friends," Mr Trump tweeted on Thursday.
Scotland Yard on Thursday identified the killer behind the London terror attack as Khalid Masood, a married father-of-three and "fitness freak".
Masood had previous convictions for assaults, including GBH, possession of offensive weapons and public order offences. He had not been convicted of any terrorism offences.
Police said the attacker was born in Kent but moved to the West Midlands.
