Her magic turns them into Twili.

It took a few hours for Midna to find the exact tome with the spell she required. During that time, Zelda waited patiently, sitting on her haunches, while Link sniffed around the room, restless with energy. "Got it!" the Twilight Princess snapped, catching the wolves's attention. Turning to her, they saw Midna smiling with a touch of that same wicked smirk she'd had as an imp. "It shouldn't take long, I'll set up the circle."

As Midna worked to prepare the material ingredients and set up the ritual circle, Link was now the one feeling more calm. Zelda, on the other hand, sneaked a peek at the spell's contents. Reading it was harder with canine eyes, but she did get the gist: a spell to return one transformed to their normal form. She saw no issues with the spell, and thus willingly entered the ritual circle as Midna started chanting the spell.

Both wolves felt the magic begin to coalesce, surrounding their bodies before invading them. Dark tendrils of Twili magic started to reshape their bodies, bipedal forms becoming upright, paws becoming hands, fur retreating into skin. It became impossible to see, from the physical darkness working the magic, until that blackness disappeared, and both Link and Zelda began blinking to try and see once more. When they could see, they saw something from the spell had gone horribly wrong. They weren't Hylians. They were Twili. Ashen grey skin, bright orange hair, and eyes that would look foreign immediately in Hyrule.