The 24-year-old was part of a 16-man break that established itself early in the 110km stage from Oyem to Bitam.
And Dockx took the victory by beating fellow escapees Abdelbasset Hannachi (GSP Algeria) and team-mate Gaetan Bille to the line.
It was a second stage win for the Belgian team after Monday’s stage winner Frederique Robert.
"It pleases me of course to win another race after four years," Dockx said. "This morning we already had a long transfer and we suspected that Europcar had a plan. There was a fast start and before we knew we escaped with 16.
"We worked very well together, but there were a lot of fast guys in the group, so we didn’t have to wait for a sprint.”
He added: “The last few days I had ridden a lot on the head of the peloton, but I feel I’m getting better and better. The next days we will try to get Gaëtan in the right escape, but if the bunch is still together in the end, there might be a sprint from Vicente Reynes or Fréderique Robert.”
Stage two winner Andrea Palini was part of the breakaway and finished seventh to retain the overall lead.
The eighth edition of Africa's only 2.1 rated race by the UCI sees nine African national teams join UCI ProTeams Lampre-Merida and Lotto-Belisol plus Europcar, Cofidis, Groupement Sportif Oil and MTN-Qhubeka in the seven-day race.