Wikipedia lists these as Thanos' powers:
Superhuman strength, durability, and endurance
Energy manipulation
Telekinesis
Teleportation
Longevity
and these as Darkseid's powers:
Omega Beams: projects concussive force or disintegrating energy
Superhuman strength, stamina, speed, durability and endurance
Super intelligence
Immortality
Invulnerability
Flight
Shapeshifting
Telekinesis
Telepathy
Teleportation
Mind reading and control
Limited time travel
So I'm going to say that Darkseid wins round one and then Thanos blinks him out of existence with the infinity gauntlet in round two.