The Spaniard started Bayern Munich's 2-0 home win at the weekend but withdrew after 62 minutes, and scans have revealed he has torn the ligaments in his right ankle.
For almost every other team on the planet, this would be a colossal loss. For Bayern, not only is it a minor blow given their squad depth, but it could also turn out to be a blessing in disguise.
Pep Guardiola faced a monumental task this summer, taking the reins at a club that had just completed a historic treble under revered manager Jupp Heynckes.
The 7-0 aggregate destruction of Barcelona, dismantling of Juventus' elite defence, ability to pull out a win at Wembley and numerous tactical advancements made the role akin to a poison chalice—whoever signs on will face scrutiny like none before.
Uli Hoeness chose Pep and secured his signature as early as January 2013 in order to give him enough time to learn German, plan appropriately and figure out a way to take an immortal team to the next level.
He started off on all the right notes, telling The Telegraph, "The players of Barcelona are different to those who play here at Bayern so I have to adapt to the players—100 per cent. The system doesn’t matter."
A resounding sigh of relief swept through Bavaria, as fears of a false-nine, tiki-taka system were instantly dissolved: The last thing diehard Bayern fans wanted was sweeping changes, and doing so could ruin what appeared to be an empire in the making.
But the tinkering did start—as early as preseason—with Arjen Robben up front, Thomas Mueller in a role approaching false-nine, Philipp Lahm in central midfield and Toni Kroos as a lone holding player.
The system he has chosen, regularly (but perhaps inaccurately) dubbed as a 4-1-4-1, is very different to the combative 4-2-3-1 Heynckes favoured.
It's important to note that Pep's record so far in the Bundesliga is perfect: played three, won three, scored six, just the one conceded. They're the reigning European champions, and the pressure is on, but Pep's shoe-horning of attacking talents into his lineup is hindering the progress made.
But as B/R's Clark Whitney argues, there are some quizzical things happening at the Allianz Arena, chief of which is attempting to put too many playmakers on the same pitch in the same strip:
Against Nurnberg, it seemed a case of too many cooks spoiling the broth.
In Franck Ribery, Mario Gotze and Thiago, Bayern had three playmakers on the pitch at the start of the match. And although the Frenchman played confidently, Gotze and Thiago looked utterly confused at times, wandering in search of any purpose.
It's no coincidence that Bayern began to look much more dangerous following the introduction of Muller for Thiago.
Thiago was a can't-miss signing this summer given his price (€20 million) and potential (world-class), but his presence has disrupted the harmony of the side just a little.
Pep is under pressure to play him, while Gotze's return from injury has doubled the headache: Is it even possible to accommodate so many playmakers in a side so soon?
Bayern achieved an astonishing 81 percent possession against Nurnberg, but it took a Ribery header—yes, header—to break the deadlock in the 69th minute.
You'd never wish any injury on a player, particularly ankle ligament damage, but Thiago's absence might just buy Guardiola a little more time to work out how this side is set to play. He still faces the issue of adding in Gotze, but his conundrum has been halved.
With the immense squad depth, Thiago won't be missed. In fact, it may just help the team settle under their new, different manager.