Uber's drivers can continue to operate in the capital while the firm pursues an appeal against the decision from the regulator, Transport for London (TfL). "We want to work with London to make things right", Uber said in a statement.
A Transport for London spokesman also called the talks constructive and said further "steps in this process will take place over the coming weeks".
On Monday Uber's United Kingdom head Jo Bertram stood down ahead of the meeting, with the company saying that her departure was not related to the non-renewal of the firm's London licence.
After the meeting Khosrowshahi tweeted a picture of himself with some Uber drivers, saying he was "determined to make things right in this great city".
Uber is used by an estimated 40,000 drivers and 3.5 million customers in London. Uber, which has been heavily criticised for lax procedures relating to reporting criminal offences, carrying out criminal records check on its drivers and verifying the drivers' medical records, intends to appeal against the decision. London Mayor Sadiq Khan, a Labour politician, supports the regulator's decision, while UK Prime Minister and Conservative Party leader Theresa May said in a BBC interview on Thursday that the city's plan threatened jobs and is "disproportionate".More news: Everton Lose At Home As The Pressure Mounts On Ronald Koeman
More news: British Airline 'Monarch' Collapses Operation, Triggers Largest Peacetime Repatriation
More news: Eagles face off against Chargers after franchise-record breaking win
A meeting between the new boss of Uber and London's transport commissioner to discuss the firm's future in the capital was described by both sides as "constructive".
Meanwhile, the chief executive of Uber rival Kabbee, a booking and price comparison service for minicabs, said Uber should also be investigated over its tax payments and market dominance.
Uber's regional manager for northern Europe has quit - barely a fortnight after the ride-hailing app was stripped of its licence in London.
Ms Bertram said in an internal email she would be taking up a "new and exciting role elsewhere".
More than 800,000 people have signed a petition calling on TfL to reverse its decision and renew Uber's license.