Zinnbauer took over on an initially temporary basis from Mirko Slomka in September and steered the then last-placed former European champions to a 0-0 draw at leaders Bayern Munich in his first game in charge.
"Joe Zinnbauer has signed a newly drafted contract to 2016," the club said on Monday.
Hamburg also managed to beat Borussia Dortmund for their first away win in almost a year.
His team are not out of danger yet, however, having also lost three times since he took over to remain in the relegation playoff spot on six points from nine league matches, two ahead of last-placed northern rivals Werder Bremen.
The club has spent heavily to bring in such players as Lewis Holtby, Nicolai Mueller, U.S. international Julian Greene and Swiss Valon Behrami.
(Reporting by Karolos Grohmann; editing by Clare Lovell)
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