The 36-year-old's departure after one-and-a-half seasons at the club was announced hours after the squad began training for the second half of the season.
"Over the last few weeks, we have begun a process of changes within the squad," said coach Markus Gisdol on the club's website.
"Among other things, this process means that we will plan without Emir Spahic for the future and it is therefore in everyone's best interests if the club and the player go their own ways."
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Hamburg signed Spahic after he was sacked by Bayer Leverkusen in April 2015 following a clash with stadium stewards. Spahic was also banned for three months by the German Football Federation.
Spahic, who has won 94 caps for Bosnia and captained them on their debut appearance at the World Cup in 2014, was a regular last season and at the start of this term.
However, he has struggled to win his way back into the team after a knee injury.
Hamburg, the only ever-present team in the Bundesliga's 54-year history, are in the relegation playoff place with 13 points from 16 games.
(Writing by Brian Homewood; editing by Sudipto Ganguly)
