Endless Space - The Vaulters have an old tradition of appointing female leaders, and their trust in this tradition has been confirmed by the faction's uncanny ability to escape, survive, and live to fight another day. Once based on the planet Auriga, they left the planet when their predictions indicated potentially cataclysmic geo-atmospheric problems. Their attempts to colonize elsewhere have only had brief success, and the notion of a permanent base has gained an almost mythical status."

http://endlessspace.wikia.com/wiki/Faction#Vaulters

and a bit more dated

Masters of Orion II - A newer race, this humanoid group was elven or fairy-like. They were a Feudal matriarchy, in which only females (the warrior caste) could join the military. Elerian mental powers were beyond compare; their males in the philosopher caste could detect everything taking place in the galaxy, from the biggest fleet to the most distant tiny planet. The females also had some strong telepathic powers. Every ship that was at least a cruiser in size had a powerful telepath who could mind-control an entire planet, eliminating the need for ground troops. The ship leaders could also see slightly into the future, giving noticeable attack and defense advantages. They could even take mental control of a captured ship and use it in the same battle against its former fleet.

http://aliens.wikia.com/wiki/Elerian

I guess you could also throw a shout out to the Hyena and the Angler fish for female domination, but as alien as they are they still are here on earth.