174 members voted to remove Khan, two more than required, said President Sard Ayaz Sadiq.
The opposition will now form a new government and the post of prime minister is expected to be taken over by the Pakistani Muslim League coalition, PML.
Tried to dissolve Parliament
The no-confidence motion comes after a troubled week in Pakistani politics.
After reports came in that the opposition in the country had agreed to declare their distrust of Khan, he decided to dissolve parliament and call new elections.
But the 69-year-old's move was annulled on Thursday by the Supreme Court of Pakistan, which ruled it was illegal.
After a lengthy process, the vote was finally held in which Khan was deposed.
Lost support from coalition parties on the military
Imran Khan has previously had a career as a cricket star and had the support of the military when he was elected in 2018. He recently lost his parliamentary majority when allies of his party PTI left the country's coalition government.
The military has also withdrawn its support from Khan after he did not accept the election of a new head of the military intelligence service.
The opposition believes that Khan has failed to bring order to the country's economy, which has been hit hard by the corona pandemic.
No Prime Minister of Pakistan has managed to remain in office for an entire term.
However, Imran Khan is the first to be ousted through a no-confidence motion.