Purchases Manager Art Werner, who was not present in court, is appealing the sentence. A Lidl branch customer in east Salonika in 2006 said he fell ill after drinking from a bottle of beer containing a 13-centimetre (five-inch) mouse.
The supermarket blamed the incident on a bottling procedure error.
The customer has already received €30,000 in compensation.
Lidl is Germany's second biggest discount chain and recently unveiled plans to expand into the United States.
The company came under fire in Germany earlier this year for secretly spying on its employees in a bid to stop shoplifting.