Ernest Sugira scored a brace for Amavubi (The Wasps), while Aaron Boupendza scored the consolation goal for the Panthers.
Rwanda dominated position from start the first whistle and they almost took an early lead, but Emery Bayisenge’s shot was parried away by Yves Moto.
The game was heading for a goalless draw in the first half when Sugira finally gave the hosts the lead in the 43rd minute.
Rwanda took a 1-0 lead into the half-time break.
Sugira completed his brace in the second minute of the second half to give Rwanda a 2-0 lead.
Boupendza pulled one back for Gabon in the 55 minute, but things got from bad to worse for the Panthers when Tchen Kabi received his marching orders for a second bookable offence.
Rwanda went on to win the match 2-1 and qualified for the quarterfinals of the Chan 2016 tournament.