The duo, both former Wales internationals, have worked alongside the Potters boss in each of his management roles, starting with a five-year spell with the national side.
|4/1||Stoke City are 4/1 with William Hill to finish in the Premier League's top half
"They are both outstanding coaches, while they also have a real understanding of the game and how I like things to be.
"So that means when you go to a new club, you hit the ground running and everybody in the squad is up to speed. I'm pleased that they are joining us because I'm sure I will benefit from that and so, too, will Stoke City."
Chief executive Tony Scholes added: "Mark Bowen and Eddie Niedzwiecki have been key members of Mark Hughes's backroom team for some time now and he was therefore eager to have them working with him once again here.
"They both have outstanding pedigree as coaches and we are delighted that they have now agreed to join Mark's new team."