It can be quite a shock seeing GPs fight for the first time, can't it? They're usually so gentle and lazy passive, and all of a sudden they turn into WWF wrestlers
I would reintroduce them outside of the cage. Whoever is already living in the cage will see it as 'their' territory, so you can't just put the other guinea back in there without a fight. Even if you move the dominant one into the other's cage, you would have the same problem, because you don't really have a 'dominant' one anymore - you had a dominant and submissive when they used to live together, but now they've both become top dog in their own domain (especially over the pups), they won't necessarily just revert back. They need to reestablish their roles and get to know each other again, and it should be on neutral territory.
Take a bit of bedding from each GP's cage and rub it on the other GP to transfer some of the smell. Then put a towel in the bottom of the bath and put them both in there, ensuring that there's something to hide under (not something out of either cage - something new) and plenty of nibbles to keep them entertained. Remember to put the plug in so no legs get caught. Keep a close eye on them, but let them squabble - stop them if you think it's really getting out of hand, but otherwise they'll need to sort it out between themselves. By stopping the fight, you're just prolonging the process. Usually the submissive one will just revert back to that position once she's been dominated by the other, but you need to let it run it's course. If you don't have a bath, even the bathroom floor will do - just somewhere that they've never been before (new smells, sights etc) and that is quite enclosed so they can't just run to opposite corners and avoid each other!
Whilst that's going on, have someone else fully clean the new cage with cage disinfectant (bars, base, bowls, beds, everything) and put fresh bedding and hay in, so it doesn't smell of either GP. Rearrange the 'furniture' so it's like a new cage (put two beds and two food bowls in for now), and then try putting them both into it. That way neither has claim over it from the beginning.
But if all else fails, you'll just have to keep them in separate cages (next to each other for company) and let them out together at play time. Oh, and get them some boxing gloves