European football's governing body UEFA had fined Hanover €15,000 after crowd trouble during a home Europa League match against FC Copenhagen in November 2011.
Hannover regional court has ordered one fan who set off a flare from the stands to pay the club €6,000, while a second supporter who ran on the pitch must pay €2,500.
"Their behaviour was reprehensible and should not be tolerated," said the judge, while the club had wanted the fans to pay the full amount of €15,000.
Both individuals will pay off the amount in monthly installments and the club's lawyer Björn Bremer was happy with the verdict.
"The economic aspect is secondary. We're concerned with the deterrent effect. It must hurt the fans in the wallet," he told Bild newspaper.
Hannover 96's success could pave the way for other Bundesliga clubs to sue fans for financial compensation in the future should they be fined for their supporters' misconduct.
In the past, Hannover 96 has had to pay out €100,000 to UEFA for their fans misconduct.
In August 2013, club president Martin Kind said: "If the fans want to cause us penalties, then perhaps they could pay for it themselves."