The 23-year-old right-back has hugely impressed since joining the Terriers on a season-long loan last summer.
Now the Premier League side have triggered the clause in that deal to turn it into a full-time arrangement for an undisclosed fee.
Hadergjonaj will now join Huddersfield on a three-year contract until 2021, with the option for a further year.
Town boss: “We knew that Flo would offer great competition for the right back position and I think his first seven months at Huddersfield Town have shown why he is so highly-rated in Germany.
“As we expected, his characteristics have been perfect for our style of play and his performances have really improved game-by-game for us.
“He is also a great guy who has fitted into our dressing room perfectly.
“We must also remember that he is only 23 years old, so he has plenty of space to improve further too.
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“That’s very exciting for everyone at the club.”
Hadergjonaj began his career with Swiss Super League outfit Young Boys.
He joined second tier Inglolstadt in 2016 before catching the attention of Wagner a year ago.
The defender won his solitary senior cap for Switzerland against Belarus in June 2017.
Hadergjonaj has become a popular figure at the John Smith's Stadium since his arrival and has provided two assists in his 19 appearances for the club.
Huddersfield and the star will be hoping he can continue his progress in the top-flight next season.
Following last year's promotion, the Terriers are currently on course to retain their Prem status.
Wagner's men are currently three points above the drop zone with nine matches remaining.
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