The Wasps dominated the first half of an exciting game, although neither team looked close to scoring.
Rwanda came up against a solid Gabonese defense, which held Morocco in a goalless draws last Sunday.
Just before half-time, Ernest Sugira stepped up to break the deadlock, when he took advantage of a loose ball in the penalty area.
The AS Kigali striker reacted quickly, and sent a low shot past a helpless Yves Moto.
The second half was only just underway when the 24-year-old doubled the score, firing a powerful shot into the top corner in front of a rapturous home crowd.
This time Moto made contact with the ball, but couldn’t prevent it from finding the back of the net.
Two goals down and having used up their three substitutes, Gabon looked dead and buried, but the Panthers responded with spirit.
Their efforts paid off in the 55th minute, when goalkeeper Eric Ndayishimiye failed to intercept a Mario Mandrault cross.
Aaron Boupendza seized the opportunity to score with a header.
A couple of minutes later Gabon almost got lucky again, when Celestin Ndayishimiye's botched attempt at a clearance forced a save from his own goalkeeper.
Down to ten men after Tchen Kabi was sent off for a second yellow card, the Panthers kept on pressing the Rwandan defense, in search of desperate last-minute equaliser.
They came close to snatching a much-needed point in the 83rd minute, when Stevy Nzambe hit the cross bar with a powerful free kick.
With six points from two games, the CHAN 2016 hosts cruise through to the quarterfinals, where they will face the runners-up of group B.
Gabon can still qualify, but they will need to win their next encounter against Ivory Coast next Sunday.