The morning rush-hour stoppage on the Central Line marked the return of fears about London's creaking transport network after the first three days of full competition at the Olympics were relatively trouble-free.
"The suspension is due to a train being taken out of service at Leyton (one stop from the Olympic Park) after the driver reported smelling smoke," said a spokesman for Transport for London (TfL), the capital transport authority.
"This has been investigated and all passengers left the train and station without reported problems."
There were no Central Line trains serving the Olympic Park station of Stratford for several hours and severe delays on the rest of the line, which goes from east to west across London.
Passengers on one packed train that was stuck at a station for several minutes laughed when they heard a recorded message from London Mayor Boris Johnson telling them to plan their journeys ahead.
London's transport network is expecting 15 million journeys to be made on each of the busiest days of the Games compared with 12 million normally, TFL has said.
But fears of traffic chaos in London have so far failed to materialise.
Authorities have taken some of the dedicated "Games Lanes" for Olympic traffic out of operation as many officials have been taking public transport instead, Johnson said on Monday.