Services came to a complete standstill from around 8pm on Wednesday evening due to the downed lines, one in Hallsberg and one in Laxå.
Trains began moving again after a couple of hours with delays ranging from three to four hours on the route.
By midnight between 25-30 trains were standing in queues waiting before they began rolling again in the early hours, although at reduced speeds.
Shortly after 5am there remained only one track open between Laxå and Hallsberg.
The backlog eased during the night but the Transport Administration (Trafikverket) expects further congestion on the tracks during Thursday as services intensify.
All trains are expected to depart as usual from both Stockholm and Gothenburg during the day, but as the trains must merge onto one track instead of two at the two locations delays will occur.
“We can’t say how long they are going to be,” Linda Bengtsson at the Transport Administration said.
“According to a very preliminary forecast Hallsberg should be ready at 9am. At Laxå, where the track has been damaged by fallen lines, a single track will operate until about 6pm,” she said.