By Rules as Written: Yes.
Player's Handbook, page 72:
When you roll a 1 or 2 on a damage die for an attack you make with a melee weapon that you are wielding with two hands, you can reroll the die and must use the new roll, even if the new roll is a 1 or a 2. The weapon must have the two-handed or versatile property for you to gain this benefit.
This is fairly explicit. If it's a damage die, and it's rolled for an attack you make with a melee weapon in two hands, then you get the re-roll. This works for Combat Superiority, Smite, bonus dice from spell buffs, and even Sneak Attack if you could figure out a way to sneak attack with a two-handed weapon (currently, there is no way to do so).
By Rules as Intended: Probably not.
Mike Mearls, one of the lead designers of DnD 5e, replied to a similar question on twitter about whether Great Weapon Fighting allowed you to re-roll smite damage. His reply was that he would rule that Great Weapon Fighting only applies to weapon damage, not smite or, by extension, combat superiority dice.
However, Mearls has stated before that he is by no means the final word on what is or is not "correct". His statement is specifically the ruling he would make, not an official response from Wizards of the Coast as a whole, so it should be taken with a grain of salt.
What Effect Would It Have
Ultimately, you have to decide for yourself whether you want to allow this to happen or not. To help aid that decision, I thought I'd share with you the math on exactly what effect this ruling would have, in either direction. For these calculations, I'm using a standardized Fighter build, and calculating how much damage, on average, they would deal to an average foe at any given level, including hit chance, critical hits, and any other relevant modifiers.
Without Using Combat Superiority:
- Level 3: 7.2 DpR
- Level 5: 18.1 DpR
- Level 11: 31.2 DpR
- Level 20: 39.0 DpR
With Combat Superiority and no reroll:
- Level 3: 10.1 DpR
- Level 5: 24.8 DpR
- Level 11: 44.4 DpR
- Level 20: 58.5 DpR
Combat Superiority with reroll:
- Level 3: 10.6 DpR
- Level 5: 26.0 DpR
- Level 11: 46.4 DpR
- Level 20: 61.0 DpR
As you can see, overall the difference is fairly minor. All told, the damage increase is never more than 5% of the total damage being done, and this is assuming that you're using Combat Superiority on all of your attacks, which is probably not what you want to be doing when you have 3-4 attacks each turn.
It's certainly a buff, but nothing to write home about, and if it makes your players feel stronger or more clever to be using their abilities in this way, then I'd say let them have it. The difference is small enough that, overall, it's unlikely to have any real impact on the game.