The firm was hit with a penalty of 10,000 litas (£2,500) by the country's media watchdog for its depiction of the fictional beer brand Duff, AFP reports.
As unlicensed Duff beer is sold in countries including Argentina, Mexico, Spain, Portugal and Germany, the governing body ruled that the publisher was in violation of the country's laws on the advertisement of alcohol.
Media Incognito has suspended publication of the title while it works towards a resolution. Bongo Comics, which holds the rights to The Simpsons in the US, allegedly does not permit alterations to the source material.
Simpsons creator Matt Groening refuses to license out the Duff trademark to brewers over concerns that it could encourage minors to drink. Fox and Groening sued an Australian drinks firm in 1995 over the matter.
Groening co-founded Bongo Comics in 1993 to publish titles based on his television projects.
> Read our latest comics news