Southern Rail reported the loss of signalling, between St Denys and Portchester, which caused lines to be ‘blocked’.
Even with these repairs, commuters have been warned that they may still face possible delays and cancellations.
A statement from the company said: ‘The fault with the signalling system has been fixed, and trains can now run as normal to and from Southampton.
‘The first train able to run through to Southampton Central will arrive at 2.03pm.
‘The first train from Southampton Central towards London will depart at 2.13pm.
‘We're working hard to return to our scheduled timetable, but your journey may still be cancelled or delayed.
‘Please continue to check journey planners and station information, and allow for extra time to reach your destination.’
At the time, services could not call at Swanwick railway station, as trains will be diverted via Eastleigh.
Earlier in the day, Southern Rail reported: ‘A fault with the signalling system between St Denys and Portchester is resulting in all lines being blocked.’
Workers from Network Rail Wessex fixed the fault, but the company warned disruption may continue.
A statement said: ‘Signalling is working well again with the exception of one signal, which may well be the cause of the original fuse blowing.
‘Thank you for your patience with us today - we're sorry to say some disruption is likely for a while longer.’