The 27-year-old joined the struggling Bundesliga outfit on a season-long loan from Arsenal in July 2013 and has started 20 league games this season.
Local media reports suggest Djourou has signed a deal keeping him in Hamburg until 2016 for between 2.5 and 3.5 million euros.
And without revealing the details, Hamburg manager Mirko Slomka confirmed on Wednesday that a deal had been done for the Switzerland international.
"I am happy that he's staying with us for the next few years as he's a stabilising influence at the centre of our defence," said Slomka.
Hamburg are in 17th place in the Bundesliga and are fighting to avoid the first relegation in the club's history.