Winger Costa returned to team training on Wednesday, a day after their 1-0 loss to Hoffenheim - only Bayern's second league defeat of the season - but completed only parts of it as he works towards his comeback from a mid-March knee injury.
With Mueller and Neuer training alone, things seemed to take a turn for the worse on Thursday when Lewandowski, who has netted 24 times in the league, had to break off training, clutching his thigh.
But the Pole will play against his former club, saying on Twitter: "Everything is fine. I will be ready."
Despite their midweek defeat, Bayern, chasing a record-extending fifth consecutive league title, still command a comfortable 10-point advantage over second-placed RB Leipzig.
But with Real Madrid awaiting in the Champions League quarter-final next week, Bayern know too well a slip-up against Dortmund could seriously dent their self-confidence.
"That was a setback at just the right time," defender Mats Hummels said of their first ever loss to Hoffenheim. "It is obvious that when we are passive in our game we are not even half as strong as when we bring a certain intensity into it.
"So on Saturday we will give it all we have," said Hummels.
Read the full article on eurosport.co.uk: Muller and Neuer doubtful as Bayern battle injury problems before Dortmund