Marius Veselis will have to pay 3000 litas ($1435), reported Reuters.
The cartoons provoked a storm of criticism in Lithuania, where 80 per cent of the population is Roman Catholic.
The commission made its decision after the Inspector of Journalists' Ethics, Romas Gudaitis, said Popetown should be banned because it portrays the clergy as destructive and incites religious discrimination.
MTV Lietuva spokeswoman Ema Segal told Reuters that Veselis would appeal. Segal said the series was aired in all the three Baltic states but Lithuania was the only one that reacted strongly against it.
MTV began airing the series in Lithuania in December, after a court rejected the Church's bid to postpone it. The Church later said it planned to sue MTV for inciting religious hatred.
"This is just an artistic satire and nothing more,” Segal was quoted as saying. “We neither attempted to mock religion nor God himself.”
According to Reuters, Veselis said in a statement last month that the reaction to Popetown had unmasked Lithuania as a "sort of half-medieval, half-communist, sick culture."
The show was commissioned by the BBC in 2002 but dropped in 2004 because of worries it might offend Catholics. There were protests against the series when it was shown in New Zealand and in Germany.
.- Lithuania’s Radio and Television Commission voted unanimously to fine the director of MTV Networks Baltic for airing Popetown, an anti-Catholic cartoon whose humor is based on irreverence toward the Roman Catholic Church.