Sir Bernard Hogan-Howe said his officers often had "limited options" in such circumstances.
His comments come after a Met police officer was filmed apparently attacking a car as the driver refused to get out.
The Independent Police Complaints Commission is investigating the incident.
The officer involved and his colleague have since been placed on restricted duties.
Refusing to comment on the specific incident, Sir Bernard said officers must consider the "gravity" of an alleged offence and what would happen if a suspect drove away.
At a meeting of London's Police and Crime Committee, he said: "If you've got a stopped vehicle and you can't get in what are you going to do - sit there all day?
"You've got to do something, so we do our best to get into the vehicle without causing any damage," he said, while admitting vehicles were "occasionally"  damaged.
The commissioner said removing suspects from a stationary car reduced the chances of a subsequent pursuit.
He added: "One of the things you've got to look at is the gravity of the offence for which you want to arrest that person."
Asked whether driving offences might constitute a reason for police breaking into a car, he said there were a number of reasons why someone might be banned from driving and a "simple motoring offence" may not always be "as simple as it appears".
Sir Bernard also discussed the difficulties of police pursuits, following a crash in Penge, south London, last month in which two people died.
He said police drones, able to monitor suspect cars from the sky, might have a "small part to play" in the future while his "ideal scenario" would be an electronic device that "slowed down" pursued cars.
The Metropolitan Police Commissioner has defended officers faced with the "dilemma" of suspects who refuse to leave vehicles.