Rivals clashed during a BBC debate last night, ahead of polling day tomorrow
He also accused the Conservative MP of telling lies and scaring people, and brandished a 'Vote Leave' leaflet which had warned that 'majority-Muslim' Turkey could join the European Union.
"That's scaremongering, Boris, and you should be ashamed … you are using the ruse of Turkey to scare people to vote Leave," Mr Khan added.
In heated exchanges in front of an audience of 6,000, Johnson hit back by pointing out that Khan had previously said those concerned about immigration should not be accused of prejudice.
He also argued that people on low incomes stood to benefit financially from leaving the 28-member trading bloc.
The former London mayor added: "In my view, as a Conservative, and I am a proud Conservative and a believer in free markets.
"I think the differentials in income in our country have become too great and I think it is wrong FTSE-100 chiefs are now earning 150 times the average pay of people on the shop floor.
"It would be a fine thing, as Lord Rose says, if people on low incomes got a pay rise as a result of us taking back control of our country and our system."
The leader of the Scottish Conservatives, Ruth Davidson, also repeatedly clashed with Boris Johnson, accusing the Leave panelists of "lying".
She attacked Vote Leave's 'take back control' slogan, warning: "You lose control by losing your seat at the table."
Davidson, who gave the closing statement for Remain, told the Wembley audience they had to be "100% sure" of their vote, adding that there was "no going back on Friday morning".
And in his closing statement, Mr Johnson declared: "Thursday can be our country's Independence Day" if the UK votes to leave.