Poland's top-flight Ekstraklasa league said it punished Stilic for leading Lech fans in an offensive chant during an end-of-season celebration in Poznan on Sunday.
The ban will come into force next season, and applies to any European league, potentially denting the 24-year-old's attractiveness to a new club.
Stilic, a member of the Bosnia squad who were one of the surprises of the Euro 2012 qualifying campaign and made it as far as the playoffs, has said he wants to leave Poland after four years at Lech.
The player was also fined 20,000 zloty (4,700 euros, $6,100), a relatively high individual penalty in Polish football terms.
There is little love lost between supporters from the western city of Poznan and those in the capital Warsaw, and Lech's fans were ecstatic after Legia failed to clinch the league title.
Legia finished behind champions Slask Wroclaw and runners-up Ruch Chorzow, but while Poland has three berths in European competition, fourth-placed Lech secured one because Legia had already won the Polish Cup and earned an automatic Europa League slot.
Among other decisions, the Ekstraklasa's disciplinary body fined Legia 70,000 zloty after its fans set off flares and hurled them onto the pitch, forcing an eight-minute halt to their season-ender at home to Korona Kielce.
Legia have repeatedly criticised a hardline section of their fans for racking up fine upon fine, hitting the club's coffers.
Hardcore supporters were enraged after Legia lost their hold on the top of the league table due to a slump in form, and reportedly waylaid the team bus as the side returned from the season's penultimate match.
Stilic hit with six-match European league ban
Advertisement