Sowter, who was born in Australia but qualifies as non-overseas due to a British passport, had a spell on loan at Durham during last summer's Vitality Blast, taking eight wickets in seven matches.
"It is great that we have been able to secure Nathan Sowter to Durham for next season," Marcus North, Durham's director of cricket, said. "Nathan impressed during his loan spell in the summer and will bring a wealth of experience and quality to complement our current spin options in the shorter format."
Sowter was Middlesex's third-highest wicket-taker in T20 cricket, with 71 at 20.33 over the course of seven seasons at Lord's. He is expected to play in the One-Day Cup for Durham, depending on his involvement in the Hundred, having been in Oval Invincibles' squad in 2021 and 2022.
Sowter said: "I am really excited for this opportunity to come back to Durham after a short loan spell last season. I am looking forward to making an impact and contributing to success on the pitch with Durham."