Carsten Brzeski, chief economist at ING-DiBa, said on Monday that Germany was now "getting used to defeats" and that the vote represented another "disappointing outcome" for Merkel but that it was too early to say how the wider, federal election will go next year.
"Ahead of the next federal elections, it is clearly too early to give a decent prediction of the election results. There are simply too many open questions, like for example: will the AfD maintain its current momentum or will protest voters show their old reflex and vote much more coalition-oriented in federal elections? Will the SPD be able to use the tail wind from the state elections or weaken further? And, the most important one, could Angela Merkel simply decide not to run for a fourth term in office, as she could have had enough of the bickering in her own party?," Brzeski noted.
"Generally speaking, unless the AfD dismantles itself in the coming twelve months, the likelihood of a three-party coalition will increase as two parties will find it hard to get more than 50 percent of all votes," he noted.
Brzewski said that Merkel's CDU was continuing its recent downward trend, having suffered defeats at the last five state elections. In fact, after the Berlin elections, Brzeski noted that the CDU "will very likely only be governing in five out of the sixteen federal states. Except for the strong performance at the elections in Saxony-Anhalt earlier this year, the last convincing CDU victory at state elections dates back to 2014 (Saxony)."
"All in all, given the new – mildly put – challenging environment and increased unrest in Germany's government, politics will remain at centre-stage in the coming months. The only good news for Angela Merkel is that the next state elections are only scheduled for late-March next year," he noted.
Another analyst, Carsten Nickel, deputy director of research at Teneo Intelligence, was more sanguine about Merkel's prospects, saying on Sunday that the chancellor's re-election next year "remains highly likely" and that Merkel could start to adjust her migrant policy in response to the loss of voter and party support.
"Berlin's urban politics are hardly a blueprint for developments on the federal level," Nickel said in a note after the result. "Still, tonight's (Sunday's) result was the weakest CDU showing ever in Berlin. For Merkel, the loss of yet another regional state government means that pressure from the CDU's Bavarian sister party, the Christian Social Union (CSU), will intensify further as of next week."
"Merkel's Christian alliance will now have to carve out a migration compromise, ideally in time for their party conferences in November and December."
Follow CNBC International on Twitter and Facebook.