The incident happened Sunday afternoon when the unidentified young man and woman allegedly started copulating aboard a train, the Toronto Sun reported.
A passenger the Sun described as "disgusted" pressed the emergency stop strip and transit authorities arrived to separate the pair.
After a 14-minute delay, the couple were put off at the next station, where they allegedly resumed having sex on the floor, the newspaper said.
The station coupling was caught on video and posted to YouTube, although it has been removed and replaced several times.
Police said the two were clearly intoxicated although it wasn't clear whether it was alcohol or drug-related. They were taken to a hospital for evaluation as a precaution.
Each was charged with engaging in a lewd act, police said.