The Dortmund star is desperate not to see his fellow attacker join his side's arch rivals for free at the end of the current campaign.
The Polish striker was heavily linked with a switch to Die Roten throughout last summer but was eventually persuaded to stay with BVB for another season after the club refused to negotiate with its Bundesliga rivals.
His Signal Iduna Park contract expires at the end of the current season and the Gabon international is hoping he will not join his side's fierce rivals.
"If Lewandowski leaves, we would prefer him to join Barcelona rather than Bayern Munich,” the Gabonese international told beIN Sport.
The 24-year-old also revealed that he rejected the advances of Paris Saint-Germain over the summer owing to his desire to experience a different league after five seasons in France.
“There are stars in Paris and of course we talk about them in Dortmund," he said. "There was contact after me personally, but as I already said it was too big a project for me and that's why I went with something else. They have a great project but I was more taken by the prospect of Germany, a change of scenery. I wanted to leave France.
"They [PSG] are a great team, it's a pleasure to see them play. I watch them from time to time. There are some big names offering some beautiful football.”
Aubameyang netted his second goal in as many games on Friday in Dortmund’s 6-1 hammering of Stuttgart.