There was no word on possible suspects but the incident is being considered by Russian authorities as a "terrorist" attack.
The federal investigative committee said the bomb exploded with the force of 200 grammes of TNT at most, and left a metre-wide crater on the railbed but did not damage the engine.
The blast occurred before dawn near St Petersburg's Baltic Station on a line to Belarus, Russian Railways officials said.
At least 37 people were killed in late November after a bomb exploded on tracks between Russia's largest cities.
A group of fighters from Russia's North Caucasus had claimed responsibility for the attack on the Nevsky Express and vowed further "acts of sabotage".
However, no major attacks followed.
Traffic halted part of the line near the blast site, Russian Railways said.