Assistant manager Bowen and first-team coach Niedzwiecki have been widely expected to join Hughes in the Potteries since he succeeded Tony Pulis last month, having previously worked together with Wales, Blackburn, Manchester City, Fulham and QPR.
The news was confirmed and Hughes said: "They're the best at what they do in my opinion. That is why they have worked alongside me for so long.
"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."