Heynckes replaced Jurgen Klinsmann on Monday after the 44-year-old was sacked following Bayern's 1-0 home defeat by Schalke 04. They are third in the league, three points off the top with five matches left.
Bayern are already out of the German Cup and the Champions League and failing to finish in the top two, missing automatic qualification to the top European competition, could spell financial disaster for the club.
"The aim must be direct qualification for the Champions League. I can help with my experience and my know-how in this present situation," Heynckes said.
"We should not think about the title, let alone talk about it," Heynckes, 63, who coached Bayern from 1987 to 1991, winning two championships, told the club's website.
VfL Wolfsburg lead the standings, with Hertha Berlin two points behind on 55. Bayern, VfB Stuttgart and Hamburg SV are on 54.
Heynckes, a former striker, won the Champions League as coach of Real Madrid in 1998. His most recent coaching stint ended in mid-season when Borussia Moenchengladbach went 13 games without a win in the 2006/7 season.
Heynckes said he had not planned for such a job but had agreed to it as a favour to Bayern manager Uli Hoeness and the club that helped him progress in his coaching career.
"Bayern mean a lot to me. I am confident it will work," Heynckes said.
His first match will be against relegation-threatened Borussia Moenchengladbach, a club he played for and coached.
"This is obviously not a dream start. This is everything but comfortable," he said.
