The companies did not state the reason for the decision, but company representatives unofficially said the move is connected to a possible terrorist threat.
The cellular operators plan to resume services in the metro from 12 a.m. Thursday if there are no additional recommendations from authorities.
Russia's National Anti-Terrorism Committee, headed by Federal Security Service's (FSB) boss Nikolai Patrushev, said Tuesday the service had obtained a report from foreign sources of a possible terrorist plot to attack ground transport and one of the country's subway systems.
No indication was given as to which country issued the warning.
Russia's international cooperation on anti-terrorism involves contacts with many countries, including the United States.
Federal Bureau of Investigation spokesman Stephen Kodak declined to comment on whether the FBI provided Russian authorities with the warning, saying the bureau never comments on exchanges of information with foreign intelligence services, adding that it is up to its foreign partners to decide whether to disclose their sources.
While the report is being verified, Patrushev has issued orders to federal and regional anti-terrorism headquarters to keep on high alert and take all necessary search and preventive measures.
The country's main subway is in Moscow, but Russia also has metro systems in several other major cities.
Anti-terrorism policing has been stepped up in the Moscow Metro, and Wednesday morning reports said the FSB's regional departments throughout Russia have been put on high alert to forestall any attacks.
The national security service has also recommended that heads of passenger transport companies take pains to ensure people's security, and advised passengers to be vigilant and inform police of anything suspicious.
Alexander Gavrilov, spokesman for Moscow's Education Department, said all organized trips of schoolchildren on public transport have been canceled until further notice.
Russia's defense minister, Sergei Ivanov, told journalists that his ministry has reinforced security around especially important military and state facilities.
Reports are coming in from all over Russia that security measures have been reinforced on public transport to prevent a possible attack.
Two bomb explosions in Moscow's metro system in 2004 killed a total 49 people and injured more than 300.
A bomb detonated in a train carriage between the central metro stations Avtozavodskaya and Paveletskaya in February, and in August another went off near the entrance to Rizhskaya station in northern Moscow.