The first train left Montparnasse for Chartres at 5.33am and high-speed TGV traffic started shortly afterwards, with a train for Bordeaux, which left "a few minutes late, but it did leave", according to an official.
The half day without trains came four months after traffic in and out of Montparnasse was interrupted for three days because of a signals failure, causing major disruption for commuters and long-distance travellers.
Some TGV connections to Nantes, Bordeaux and Rennes were maintained on Sunday, leaving from Paris's Austerlitz station.
Morne announced that she had summoned Bontet at 9.00am on Monday morning to explain the "reasons for this new incident and the measures he proposes to take to draw the consequences".
Major work is taking place on the Paris regional rail network at the moment and part of Europe's busiest line, the RER A, was closed for three days at the end of October because of flooding caused by work on a nearby line.
Morne on Monday demanded a new plan for the management of works before the end of the week.