Pep Guardiola obviously came into the Pokalfinale with some extreme constraints on team-sheet selection: missing Schweinsteiger, Thiago, Alaba, Mandzukic; Ribery announced as unable to start or play a full shift; Shaqiri on the bench but likely not match fit (not blocking anyone, since Bayern didn't even name a full bench for the match)--and things got even worse when he lost captain Phillip Lahm to injury early in the match. He responded with unorthodox formations and numerous players out-of-position, and to my eyes the team responded extremely well.
Since these were formations/tactics we hadn't really seen at any point this season, it's natural to assume it was a one-time desperation ploy, but I think there are some reasons to believe we may see them again in the future at least on occasion (and remember, Pep hasn't had a fully healthy and fit squad to select from at any point this season). First a review of the formations as I saw them during the match (just going from memory--haven't rewatched it).
Bayern came out in what I'd call a 3-4-2-1, like so:
--Boateng - Javi - Dante-----
PEH - Lahm - Kroos - Rafinha
Novel aspects included the use of a back 3 (although as I'll discuss later, we do frequently show this look in possession when nominally playing 4 at the back), PEH as a wingback, Rafinha on the left, and Robben up top as CF (where most seeing the teamsheet would have assumed Muller up top and Robben on the right--although again they interchange so much normally that we've certainly seen them spend time in this shape).
After Lahm was forced to exit and Ribery came on, it initially looked like Bayern shifted into something like Juve's 3-5-2, with Kroos in the deep-lying Pirlo role and Ribery/Gotze ahead of him as CMs:
----Boateng - Javi - Dante----
PEH - Gotze - Ribery - Rafinha
--------Muller - Robben-------
However within 10 minutes or so it looked as though they had shifted again, pushing Ribery forward, into something I'd best describe as a 3-3-1-3 (not exactly a copy of Marcelo Bielsa's, but that's probably the closest thing out there):
--Boateng - Javi - Dante--
PEH --- Kroos --- Rafina
Muller - Robben - Ribery
While the front four continued to interchange, that was the basic shape for the rest of the match, including when DVB replaced PEH (pushing Boateng to RWB...to great effect on the game-winner) and when Pizarro relieved Ribery (with Robben moving out to LW).
So, after all of that, why do I think we might see this again, and not just when Pep is one injury away from having to pull on a jersey and jog onto the pitch?
First, we know Pep has identified Bielsa as a major influence, and the 3-3-1-3 approach during the second half wasn't that different from how his Barca teams would sometimes play in possession. Think Javi::Busquets dropped deep between CBs, Kroos::Xavi as deep-lying playmaker, Gotze::Iniesta as advanced playmaker. [for what it's worth we've also seen Bayern play a similar shape in possession, even under Jupp, with one of Javi/Basti dropping between the CBs]
Second, Pep experimented some with a back 3 during preseason, as well as with Lahm and Alaba advanced into midfield (Lahm's move obviously continuing throughout the season), and both of them are actually ideal fits for the wingbacks in a 3-3-1-3 (who need to be able to tuck in next to the holder [Kroos, Thiago, or Basti] as CMs in addition to the normal wide defending and attacking roles).
Third, it would explain all the rumored interest in CBs (and in a particular style of CB: pacy and aggressive in attack and defense, which fits with the extra ground they need to cover in a back 3). If Bayern semi-regularly played with 3 CBs, you could hypothetically find minutes for all of, say, Dante, Boateng, Javi, David Luiz, and Mehdi Benatia (just as a Juventus makes use of all of Chiellini, Barzagli, Bonucci, Caceres, and Ogbonna). Otherwise it's hard to fit more than 3 regulars plus an emergency option (like DVB this year).
Anyhow, it'll be interesting to see how it works out next season. Back 3s are ubiquitous in Serie A and on the upswing in the Premier League (most notably at Brendan Rogers' Liverpool) but at the moment essentially unheard of in the Bundesliga. Could we see that change in Pep Guardiola's second season at Bayern?