Barack Obama fined over London congestion charge
He and Mr Obama exchanged "points of view", he said, over £5.2m worth of unpaid congestion bills when they met.
The US Embassy said it was exempt from paying "direct taxes" but the mayor maintains the charge is not a tax.
Transport for London has confirmed that the Presidential convoy was charged but the bill has not been paid.
Mr Johnson said: "Unlike the Pope where we didn't charge the Popemobile because we closed the roads, when The Beast rolled through London that Beast paid a congestion charge.
"But on the wider principle of US and other diplomats following on the lead of the majority of good embassies in London, who pay the congestion charge, a discussion was had, points of views were exchanged, I would say that discussions were ongoing."
Several embassies refuse to pay the £10-a-day charge for driving in central London, claiming they are exempted from local taxes.
The total bill stands at £51m and the US, Russia and Japan are the top three in the list of non-payers.
In a statement, the US Embassy said it "conscientiously abides by all UK laws, including paying fines for all traffic violations, such as parking and speeding violations".
"Our position on the direct tax established by Transport for London in 2003, more commonly known as the congestion charge, is based on the 1960 Vienna Convention on Diplomatic Relations, which prohibits the imposition of this sort of tax on diplomatic missions," the statement added.
Mr Johnson has said previously that the levy was not a tax but a charge for services.
Source: bbc