Yes they do. AGP Pro just adds more power supply contacts, so that hungrier cards can pull more amperes without burning the contacts.
The one thing to look after is card alignment. AGP Pro slots are longer, and you need to align the card to the inner end of the slot (away from the outside connector end of the card). AGP Pro mainboards usually have a little plastic bit in the extension part of the slot that prevents you from screwing up at this moment.