The Ivory Coast forward had been on loan at Utrecht since January, helping the side finish fourth in the Eredivisie last season and has previously played for the club, from 2015 to 2017.
Haller said: "I'm happy and satisfied. There was a lot of interest from other clubs this summer, but for me there was only one ideal scenario, and that was Utrecht.
"Last year we built something great and I want to continue to be part of that story."
Haller joined Bundesliga outfit Dortmund three years ago, but was diagnosed with cancer and underwent two operations and chemotherapy.
Dortmund sports director Sebastian Kehl said: "Sebastien has written a special story here. He battled his cancer with impressive strength.
"Now he is returning to Utrecht – to a club that means a lot to him and for which he has regularly played in recent months. We wish Sebastien all the best for the future and, above all, good health."
He also had spells at West Ham United and Eintracht Frankfurt and helped Ivory Coast win the African Cup of Nations on home soil in 2023.
Bayer Leverkusen have secured a season-long loan deal for Manchester City's 19-year-old attacking midfielder Claudio Echeverri, outpacing rivals Borussia Dortmund in the race for the Argentine talent, according to Sky Germany.
Inter Milan have redirected their transfer focus to Benfica midfielder Florentino Luis and Borussia Dortmund forward Felix Nmecha as they aim to bolster their squad before the transfer window closes.
Borussia Dortmund narrowly escaped an upset in their DFB-Pokal first-round match, edging out third-tier Rot-Weiss Essen 1-0 at Stadion an der Hafenstrasse.
Borussia Dortmund and their striker Sebastien Haller are locked in negotiations to end his contract early, with a potential move back to FC Utrecht on the horizon.
