The 31-year-old, who had been on loan at FC Utrecht since the start of the year, ends a rollercoaster spell with Dortmund, having recovered from cancer to return to action.
He was diagnosed with testicular cancer shortly after joining the club from Ajax Amsterdam in July 2022. The striker underwent two surgeries and chemotherapy in the ensuing months before returning to play in early 2023.
He featured in a total of 33 Bundesliga matches, scoring nine goals.
“Sebastien has written a special story here. He battled his cancer with impressive strength," said Dortmund sports director Sebastian Kehl.
"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."
Haller looking forward to European football
Haller is delighted with his return to Utrecht, who are looking to qualify for the UEFA Europa League as they meet Bosnian side Zrinjski Mostar in the play-off round.
"There was considerable interest from other clubs this summer," said Haller, who joked that he's 91 per cent fit, hinting at his kit number from last season.
"However, for me, there was only one ideal scenario, and that was FC Utrecht. We have built something remarkable over the past year, and I would like to continue to be a part of it."
"When you consider our achievements in Europe, it has been exceptional. Excellent matches, significant results. The only thought is: I would like to be part of that, to assist the team. And now, that has been achieved."
Haller played for Utrecht early in his career from 2015-17.