The Dutchman watched on as his side were easily beaten 4-2 by bottom club Eintracht Braunschweig on Saturday, leaving them only one point off the bottom with 13 games remaining.
Speculation had been rife in the build-up to the game that the head coach could lose his job, and, after the disappointing defeat to their fellow relegation strugglers, sporting director Oliver Kreuzer confirmed Van Marwijk had been relieved of his duties.
"It is with regret that we were forced at this time to make this decision," he said in a statement on the club's website. "We thank Bert van Marwijk for his work."
When Van Marwijk took over from Thorsten Fink at the club in September there was an initial improvement, but they have since tumbled down the table at an alarming rate.
In their last seven league matches, Hamburg have scored five goals and conceded 20 - a run of form that has seen the 61-year-old lose his job.
Assistant Roel Coumans has also been released.
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