Dortmund dislodged Bayern, who beat Hanover 96 2-0, from the top of the table after a 6-2 victory over Hamburg.
It means Dortmund go into the international break for the forthcoming World Cup qualifiers two points clear of European champions Bayern.
Lewandowski did gain one concession to his contract which runs out in May 2014, negotiating a pay rise from 1.5 million euros ($2 million) a year to five million euros ($6.7 million) for his final 10 months in Dortmund.
Bayern coach Jupp Heynckes has been replaced by ex-Barcelona boss Pep Guardiola, Spain under-21 captain Thiago Alcantara has been recruited from the Camp Nou and Germany midfield star Mario Goetze has joined from Dortmund.
The 24-year-old, who cost Dortmund 27.5 million euros from Shakhtar Donetsk tore ligaments in his right ankle, meaning he is expected to be out for up to four weeks.
Mkhitaryan has impressed in his two friendly matches since joining Dortmund from Shakhtar Donetsk last week for 27.5m euros, (US$36m) both on his debut in Wednesday's 3-1 win at FC Basel, then Saturday's 4-1 win over Turkey's Buraspor.
Mkhitaryan will take over the midfield role vacated by Germany star Goetze's move to European champions Bayern Munich.
Borussia host Bayern in the pre-season German Super Cup on July 27 in a repeat of the Champions League, which the Bavarians won 2-1 at Wembley.
Sahin led Dortmund to the first of its consecutive titles in 2011 and then left for Real Madrid, where his career was slowed by a knee injury.
Liverpool said on Saturday they have reached agreement with Real Madrid to take the Spanish outfit's playmaker Nuri Sahin to Anfield on a season-long loan.
Liverpool manager Brendan Rodgers revealed on Thursday that he hopes to seal two more signings in the next 48 hours.
Real Madrid coach Jose Mourinho says injured forward Angel di Maria won't return before April to help cover the final stretch of the season.
Real Madrid manager Jose Mourinho has revealed that summer signing Nuri Sahin has been included in the squad for Sunday's La Liga match at home against Osasuna.
Turkey midfielder Nuri Sahin has signed a six-year contract to join Real Madrid from Bundesliga champion Borussia Dortmund.