Djourou has impressed during his loan spell with the Bundesliga side, who are now set to exercise their option to buy him on a permanent basis.
The Swiss international is expected to sign at the end of the season, and will fetch the Gunners a transfer fee of around £2million.
Djourou made his last appearance for Arsenal in April 2012, but made the loan switch after failing to dislodge the likes of Per Mertesacker, Thomas Vermaelen and Laurent Koscielny from the first team.
He completed a loan moved to Hamburg last summer, and has gone on to make 19 Bundesliga appearances this season.
The 27-year-old came through the youth system at Arsenal, signing his first professional contract in 2004.
He was never able to hold down a regular first team place however, and has previously been sent on loan to Birmingham City and Hannover 96.
Arsene Wenger has made the signing of a new centre back a priority for the summer, with reports also linking Thomas Vermaelen with a move away from the Emirates at the end of the season.