Di Matteo said on Sunday that Luiz and Cahill's fight to be fit would "probably" go right up to the day of the game as they have both been out for around a month with hamstring injuries.
Cahill insisted he would be fit for the final, saying after training: "I'm just happy that it's healed quickly. We've worked really hard, all day, afternoons, and I'm fortunate enough to be back. Hopefully, I'll be fit, I will be fit, and hopefully I'll be out there if selected.
"There's some work to be done in two or three days now leading up to the game for me to get back into it. If I need to do a little bit of other training, I'll do that. But, touch wood, there's no reaction and I felt fine out there."
But Florent Malouda was missing and Di Matteo told a packed marquee at Chelsea's training ground in Cobham: "Flo (Malouda), we'll still assess and it's going to be touch and go for him to be available for Saturday."
Malouda failed to complete the first-half of Chelsea's final Premier League game of the season against Blackburn on Sunday having strained a hamstring.
Di Matteo would be forced to complete his bench with reserves and youngsters if Luiz and Cahill were also out. "That's the worse-case scenario," he said.
"We will take some reserve-team players onto the bench, into the squad, and just figure out what to do. I've been trying different options in training and different solutions just in case."
Di Matteo has a major selection headache with four places in his starting line-up unclear.
Jose Bosingwa is likely to play centre-back if either Luiz or Cahill are not fit, otherwise he will play right-back with Branislav Ivanovic suspended.
If neither are fit and with John Terry banned then Michael Essien is likely to partner the Portuguese at centre-back with Paolo Ferreira at right-back.
Malouda would be the most likely to join John Obi Mikel and Frank Lampard in midfield as a replacement for the suspended Raul Meireles.
If he fails to recover then the Ghana international - if not required in defence - could partner Mikel in a more defensive minded midfield to counter Bayern's attacking threat with Lampard in a more advanced role in a triangle.
The only other viable alternatives for the boss if he wishes to replicate the 4-1-2-3 system he has used for most of his tenure are Oriol Romeu, although he has rarely picked the young Spaniard, or a deeper role for Juan Mata with Daniel Sturridge coming into the starting XI.
Having been left out against Blackburn, Salomon Kalou looks likely to take one of the positions on the flank in preference to Sturridge with Mata also supporting lone front man Didier Drogba.
But Di Matteo did try a 4-4-2 for the last 20 minutes against Steve Kean's side with Fernando Torres and Drogba in attack.
That system would likely see Sturridge and Mata on the flanks with Lampard and Mikel in the engine room.
Di Matteo did not think Chelsea had gained any advantage after Bayern lost the German Cup final 5-2 to Borussia Dortmund in Berlin on Saturday.
"I don't think that will have any effect on the Bayern team," he said. "They are extremely professional and they will move on from it very quickly as they know they have a big game on Saturday. I don't think it gives us any advantage."
He also played down the idea that Bayern would benefit from playing the game in their own stadium.
“"It might give them a bit of an advantage because they know the environment and the pitch, but because they are playing at home there might be more pressure on them so I am not sure it gives them a real advantage at all."