McCann was named the caretaker boss on a short-term basis after Paul Hartley was sacked prior to the Ladbrokes Premiership split.
With Dundee fighting to stave off relegation, Sky Sports pundit McCann was named as a surprise replacement, though it turned out to be a successful move.
Dundee won their first two games under McCann, before a draw at home to Ross County in his third fixture ensured the club’s safety.
It was reported that McCann had been in discussions with the board over a permanent contract, but no such deal transpired.
In a statement, Dundee thanked the 42-year-old for his efforts and for Sky agreeing to let him go for five weeks.
They insist the search for a new permanent boss is already well underway.
Managing Director John Nelms said: “On behalf of the entire Dundee Football Club family I’d like to thank Neil for his interim spell in charge. He came in and did the job we asked him to do. The club once again owes Neil a debt of gratitude. Neil is certainly a credit to Dundee Football Club and Scottish football as a whole.”
McCann himself added: “I’d like to thank everyone at Dundee FC for their hard work in the time I was manager there. It was an honour to become manager of the club where my playing career started and finished and I’m very proud I was able to succeed in keeping them in the Scottish Premiership. I wish them great success in the future.”