Merkel's center-right Christian Democratic Union (CDU) and its Bavarian sister-party the Christian Social Union (CSU) won 33 percent of the vote, provisional votes showed, down from 41.5 percent in the previous election. The pro-business FDP party, which placed fourth with 10.7 percent of the votes, has said it is open for coalition talks with Merkel's CDU. The Greens are set to join coalition talks too, which could ultimately form Germany's first four-party government in decades.
In German politics, it's usually the case that the largest party chooses the chancellor, and the second largest group picks the next post. As such, the FDP could opt for the Finance Ministry and put an end to Schaeuble's eight-year reign.
The future for Schaeuble is "the question" from a market perspective, Carsten Nickel, managing director at Teneo Intelligence, told CNBC Monday.
"In the end, I think there is probably very little alternative to Schaeuble, right now, at least in terms of individual politicians. There's nobody who really comes to mind as the key person who would challenge him for that role. I wouldn't be surprised if he stays on in the end," he said.
If Germany were to lose Schaeuble as Finance minister, the current momentum for further euro zone integration could also be damaged.
"What it means for Germany's stance on further euro zone integration is too early to tell. If the FDP will join a coalition, expect a much slower integration process and many cold showers for (French President Emmanuel) Macron," Brzeski said, referring to plans from Macron to deepen economic and financial ties.
"I don't think that the FDP can implement its own views, but it will definitely slow down any new steps towards more integration," he added, given the FDP's view goes against what Macron and other EU leaders want to implement.
The 75-year-old Schaeuble hasn't given any signs that he is ready to retire from politics. If he loses the Finance Ministry, Merkel could still appoint him as the next speaker of the German Parliament. The role would include fewer powers from those that Schaeuble currently has, but it could become more important now that the right-wing Alternative for Germany (AfD) party won its first ever parliamentary seats.