Home Secretary Sajid Javid tweeted: "I can confirm Julian Assange is now in police custody and rightly facing justice in the UK.
"I would like to thank Ecuador for its cooperation & metpoliceuk for its professionalism. No one is above the law."
Mr Assange, 47, had refused to leave the embassy, claiming if he did he would be extradited to the United States for questioning over the activities of WikiLeaks.
Scotland Yard said it was invited into the embassy by the ambassador, following the Ecuadorian government's withdrawal of asylum.
Mr Assange would remain in custody at a central London police station, before appearing at Westminster Magistrates' Court "as soon as is possible", the statement added.
UK foreign minister Sir Alan Duncan said the arrest followed "extensive dialogue between our two countries".
It comes a day after Wikileaks said it had uncovered an extensive spying operation against its co-founder at the Ecuadorean embassy.