The accident happened shortly before 9am and affected all rail traffic, northbound and southbound, between the two cities.
Sweden's Transport Administration (Trafikverket) said passengers travelling via the stations Södertälje C, Stockholm City, Uppsala C, Stockholm C, Märsta and Arlanda C could be affected by the problems.
A bridge specialist examined the flyover at 9.45am to determine whether or not it was still safe.
Traffic resumed at 10.40am.
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