Captain Chancel Mbemba headed home the opening goal in the fourth minute, and Yoane Wissa added a second 18 minutes from time in Kinshasa on Thursday, although the scoreline might have been more emphatic after they twice struck the woodwork and also had two efforts ruled offside.
It was the first game for the Congolese after advancing through the first phase of the World Cup for the first time and running England close in their last-32 tie in Atlanta in July.
However, there was no opportunity for home supporters to celebrate their achievement as the size of the crowd at the Stade des Martyrs was restricted to 20,000 after sanctions for fan violence that followed defeat by Senegal in World Cup qualification one year ago.
Mauritania and Namibia were also winners in Thursday's early games, while Libya netted a last-gasp penalty to salvage a 2-2 draw at home to Botswana behind closed doors in Tripoli, where the stadium was also banned because of previous supporter violence.
Botswana striker Tumisang Orebonye scored a double in the first half to put his side on course for a rare away win before Maruwan Alhibeeshi thrashed home from the edge of the area to pull one back in the 87th minute.
Botswana substitute Mothusi Cooper gave away a stoppage-time penalty with a clumsy challenge, allowing Ezoo El Mariamy to rescue a draw.
Mauritania won 3-1 over the Central African Republic in Casablanca, Morocco, which included a superb chipped effort over the goalkeeper from Dawda Camara, while Betuel Muzeu scored the only goal as Namibia edged Congo.
Later on Thursday, World Cup competitors Ghana and Ivory Coast play a derby in Bouake, while Cameroon host Comoros.