The workers had been on the ninth successive day of strike action that has crippled the underground system.
The conservative-led government used an emergency law to threaten the strikers with arrest unless they went back to work. It was not clear if the move would lead to transport resuming.
Strikers are opposed to proposals which might see their salaries slashed.
The operation took place shortly before 04:00 local time, with around 100 riot police officers entering the depot where workers had barricaded themselves in overnight.
A police spokesman said three people were arrested and subsequently released. The area around the depot has now been cordoned off to prevent others from joining the strike.
Bus drivers and railway workers were to join the strike on Friday. Transport unions say they will continue their action, raising the possibility that some could face arrest and criminal charges, with a prison sentence of up to five years.
The government is using civil mobilization legislation, which has only been invoked nine times since the collapse of Greeceās military dictatorship in 1974.
Workers on the underground had been striking over a public sector unified wage scheme that would see their salaries reduced by up to 25%.
Public opinion is split over the issue, but with commuters facing long taxi queues as temperatures fall, the government feels that it may just get the support it needs to hold firm.
Greece has been kept solvent by huge rescue
loans from its EU partners and the IMF since May 2010.
So far, the European Central Bank, International Monetary Fund, and the European Commission have pledged a total of 240 billion euros ($315 billion) in rescue loans, of which Greece has received more than two thirds.
The Greek government required the bailouts because it was struggling to meet the interest payments on its existing debts.
Under the terms of the rescue funds, Greece is having to agree to substantial spending cuts, such as redundancies and pay freezes in the public sector, and reduced pensions.
This is having a major knock-on impact on the wider Greek economy, with the unemployment rate hitting 26.8% earlier this month, the highest figure recorded in the EU.
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