The match was switched to the French city and played without spectators after authorities in Cadiz, the original host venue, called it off, citing public health concerns linked to an Ebola outbreak in the central African nation.
After a goalless first half, Dario Osorio put Chile ahead in the 52nd minute, and Matias Sepulveda added a second four minutes from time. Joris Kayembe pulled one back for the Congolese side in the 88th minute.
US officials have told teams that players and staff must have been outside the DRC for 21 days and symptom-free before entering the country for the World Cup.
Congo are due to travel to their tournament base in Houston on Thursday and open their Group K campaign against Portugal six days later. They then face Colombia in Guadalajara on June 23rd and Uzbekistan in Atlanta on June 27th.