To get an overall winner, this epic confrontation should be broken down a little, rather than just going in straight at the "It just wins because..." level.
We shall engage in 3 battles. The first at ground level with the troops, beasts and weapons of the respective genres. The second shall be a battle of the greatest warriors, leaders and representatives. The third shall be a titanic, cosmic battle with no holds barred. Begin:
Round 1:
Star Wars battle droid army gains an early lead over Sauron's orc army, due to the range of their energy weapons. Elves join the fray but their arrows are unable to injure the metallic menace. Star Trek personnel beam in and out of battle, killing dwarves with their phasers but taking very little damage in return.
A horde of undead zombies, led by a lich are able eventually to push back the robots, but some Predators join the fight and make short work of them.
Winner: Sci-Fi
Round 2:
Luke Skywalker and Yoda start jumping about the place, throwing their lightsabers every which way. Rand Al'Thor balefires them. Neo and Morpheus dodge the balefire in bulletime and are about to use their Kung Fu when Belgarath the Sorcerer wills their modem connection to go offline, disconnecting them.
Spock sneaks up on Belgarath and drops him with a nerve pinch just as Arnie the Terminator kills Rand Al'Thor with a one-liner (and pulling out his spine). Gandalf and Pug appear out of nowhere and with waved hands and staves, Spock and the Cyberdyne Systems T-101 are disintegrated.
Winner: Fantasy
Round 3:
As the Covenant armada begins razing the surface of different continents and the Death Star begins charging up it's main laser, Garion, with the Orb of Aldur gathers his will and says "Burn". They explode into flame.
The Reapers finally arrive through a Mass Relay but without Shepard, who was inadvertently killed by a Beholder in the previous round, the Reapers are able to roam unchecked. The Bhaalspawn, fresh from his fight with Melissan fancies one last hurrah. The Reapers start talking in deep voices while the last child of Bhaal unleashes various spells including Time Stop, Abi Dazim's Horrid Wilting and Comet. Abi Dazim has no effect as there is no moisture in the Reapers, but being hit by comets does the trick.
Jean Grey as Phoenix and Galactus unite to strike the killing blow against fantasy once and for all but Thomas Covenant and Sparhawk with the Bhelliom wipe them out before they enter the solar system.
Winner: Fantasy
Overall Winner: Fantasy
It seems sci-fi doesn't have an answer for the unbridled might of fantasy's hardest hitters, though at ground level, the superior technology, communications and shields/teleporters give them a clear edge. But after the troops are done, fantasy's greatest heroes make short work of them and their leaders and generally with little more effort than concentrating.
The laser may be mightier than the sword but magic is mightier than technology!