Guerreiro was forced off in the 17th minute of Saturday's Bundesliga clash with Stuttgart, and the Munich giants have now confirmed that he is facing a spell out with an ankle injury.
Bayern have put a timescale on his absence, but he will definitely be missing when Thomas Tuchel's side head to Real Madrid for the second leg of their European Cup semi-final.
"FC Bayern will have to make do without Raphael Guerreiro in the next few matches. The Portuguese sustained a ligament and capsule injury in his ankle in Saturday's Bundesliga match away at Stuttgart, as confirmed by a scan by the FC Bayern medical department," read a statement from the German club.
Dier, meanwhile, suffered a head injury during the same match when he produced a goal-saving header.
Raphael Guerreiro out, Eric Dier a doubt for Real Madrid game
The Englishman, who is on loan at Bayern from Tottenham Hotspur, was left with a cut on his head earlier in the contest, and it then reopened when he kept out an effort from Serhou Guirassy in the Bundesliga affair.
Dier was bandaged up and played on until the interval, when he was replaced.
After the match, Bayern head coach Tuchel provided an update on the situation, with the centre-back now regarded as a doubt for the game in the Spanish capital.
"Eric had to get stitches to the head wound that then opened up again so we at some point said it was enough. We did not want to risk it," Tuchel told reporters.
The German also revealed that Dier had been carrying a thigh problem but insisted that the reason for his withdrawal on Saturday was the head injury.
Bayern have defensive issues ahead of trip to Madrid
"Dier felt a bit something in his thigh before the game, but that wasn't the reason (he got subbed off) - it was due to the head knock. We couldn't take any more risks with him," he added.
"We then took a risk with Upa (Dayot Upamecano) who wasn't supposed to play for more than 30 minutes. This has unfortunately been the story of our season."
Matthijs de Ligt has also missed Bayern's last two matches due to a knee problem, and it remains to be seen whether he is involved against Real Madrid.
Should Dier and De Ligt fail to make it, Upamecano is likely to play alongside Kim Min-Jae in the middle of the defence against Real Madrid.
Leroy Sane and Harry Kane were on the scoresheet for Bayern in the first leg of their semi-final with the La Liga champions, while Vinicius Junior netted a brace for the Spanish outfit.