A subsidiary of Apple Inc. illegally charged customers more than $5 million in Illinois sales tax on software, a Chicago boutique alleged in a federal class action complaint.

Florodora Inc., a downtown vintage-inspired boutique, filed the complaint against software company Claris International Inc. to require it to inform class members—buyers of the software—of the illegal tax on their Filemaker Pro software purchases and to pay restitution. It also seeks to stop Claris from continuing to charge the tax.

Filemaker Pro software is a relational database to help streamline operations for businesses.

Claris charged licensees sales tax in violation of Illinois...