Hamburg, who have never been relegated from the Bundesliga, lost their fifth league game out of six on Saturday, slumping to a 1-0 defeat to Borussia Monchengladbach in front of a home crowd.
"In the last two days following our defeat to Gladbach and following a number of intensive discussions we are convinced that we needed to take this decision," said sports director Frank Arnesen, who on Saturday had backed the coach to stay on.
"As of today we will start the search for his replacement."
Oenning, 45, who took over late last season, will be replaced temporarily by reserve team coach Rodolfo Cardoso.
"I can understand that the club wants to take a different direction now," Oenning said in a short statement after a meeting with the board.
Hamburg won Oenning's first game in charge last season but have failed to win since in 13 consecutive games.
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