Poland striker Lewandowski, whose contract with Borussia expires in 2014, confirmed last week he wanted to leave BVB and said he was close to joining "the club of my choice", believed to be Bayern.
However Dortmund, desperate not to lose the 24-year-old to Bavaria after Mario Götze agreed to join Bayern in April, have scrapped the deal.
Borussia's chief executive Hans-Joachim Watzke told Bild: "Robert Lewandowski will definitely not make the switch to FC Bayern in 2013. That's final. We have informed Robert and his agents now."
It is an essential stand from BVB, who were eliminated by Bayern from the DFB-Pokal Cup, finished runners-up to them in the Bundesliga and lost the Champions League final to Jupp Heynckes' treble winners.
For Bayern, it is a belated rebuttal from a fellow domestic side. Schalke reluctantly sold goalkeeper Manuel Neuer to the five-time European Cup winners in 2011 when they would have preferred the German number one to move abroad.
Similarly, Dortmund will be eager to offload Lewandowski abroad, where he will not be short of takers.
Manchester United bid for the Pole last year and Chelsea are also interested in the striker, who finished behind only Cristiano Ronaldo in the Champions League's goals chart.
Former United boss Sir Alex Ferguson actually suggested Lewandowski's four-goal display against Real Madrid in the Champions League semi-finals was detrimental to his hopes of a Bayern move.
"I am not sure Lewandowski will be sold to Bayern now," Ferguson said in April. "The Dortmund fans are not going to be happy and I don't think they will sell to their main rivals. I think they will either let his contract run out, or sell him somewhere else."
Dortmund fans' reaction to the Götze deal was so toxic security had to be tightened at the club's training ground and the 20-year-old's brother was abused at school.