The strike, which started late Tuesday, reached its peak during the Wednesday morning rush hour when tens of thousands of commuters had to take to traffic-choked highways to get into the capital or work.
Many workers had taken precautions and even though long traffic jams were reported early Wednesday, they were not as bad as initially feared.
Both Thalys and Eurostar cancelled services to the Belgian capital.
"In Brussels, the strike is a success, around 80-90 per cent of the people are on strike," said Philippe Peers of the socialist CGSP trade union. "Many of the stewards as well are on strike, so I can tell that there will be not a single train in Brussels."
Rail service was expected to resume late Wednesday and be back at full service on Thursday morning.
Despite the weeklong warning, it still caused plenty of hardship.
Georgina Saldena, a Mexican tourist, was heading for the Paris-Charles de Gaulle airport. "Until today, we thought we had to go there by train," she said after she was surprised by the strike. And as tourist, she felt stranded with few indications for alternative options. "There is no sign, nothing that says that we have to come here to take a bus," she said at a bus stop that would take her to Paris, Saldena said.
Matthieu Regibout, who works in Brussels, said he took the last train on Tuesday, and slept in the office, to avoid the strike's effect.
Rail workers are fearful their employment conditions will be undermined under a new plan to revamp and streamline the three companies currently overseeing train traffic in Belgium.
Unions want to go back to a single company controlling the rail grid and train traffic, saying the numerous and lengthy delays of the past could be blamed on managerial disorganization.