The three far-right politicians have been charged with incitement of hate crimes and defamation, a Berlin district prosecutor's office spokesperson said on Tuesday.
The title page of the World Cup schedule pamphlet in question featured an image of a man dressed in German national team uniform with the jersey number 25. This number belonged to Owomoyela, who has a German mother and a Nigerian father. Above the image stood the phrase, "White, not just a jersey colour! For a real national team!"
The racist slogan refers to the traditional colour of the German national team jersey and the fact there have been few non-white players on the national team until recently.
Prosecutors allege that the three NPD party members are responsible publishing the pamphlet.
"They aimed to convey that that player as well as other players who do not have white skin were not worthy to represent Germany as international players," the prosecutor's office said in a statement.
New brochures later appeared with a cartoon showing one white and 10 non-white players with the caption, "National team 2010?"
The indictments are the latest in a series of legal challenges to the NPD, which holds seats in the legislatures of two eastern German states.
In February, the NPD's treasurer was arrested for allegedly embezzling more than €600,000 ($935,000) from the party's coffers and last year a party leader in Hamburg was charged with Holocaust denial.
The prosecutor's office said no trial date has yet been set. If convicted, Voigt and the two other co-defendants could face up to five years of prison or house arrest.