The Bavarian district chief behind Thursday's journey to Berlin, Peter Dreier, had called it an "act of desperation" as his southern rural area buckled under the strain of a mass influx that brought 1.1 million migrants to Germany last year.
The coach had arrived on Friday evening after a 570 kilometre (350 mile) trip outside the chancellery building of Merkel, who declined to send her staff to negotiate with the provincial official.
Berlin city representatives instead went on board and offered the group of men emergency accommodation for a night.
In absurd scenes, some 100 journalists, as well as a sprinkling of anti-Merkel protesters, stayed in a throng around the coach for two hours, while tense-faced Berlin and Bavarian officials negotiated inside, and refugees watched the TV cameras with anguished expressions.
In the end, the bus left with a police escort, and Dreier told the press he was disappointed Merkel's people hadn't come to talk to him.
He said he would pay for a night in a hotel for the group, out of his own pocket.
On Friday morning, the bus was back on the road to Bavaria, to the southern town of Landshut, which had organised the high-profile trip - with the refugees inside described as angry and disappointed.
Berlin Mayor Michael Maeller called the trip a sign of a "breakdown of solidarity" in how local governments handle the migrant influx, while Bavarian Social Democrats leader Florian Pronold condemned the "PR stunt".
Only one of the Syrian men - all of whom have official asylum status and are free to move anywhere in Germany -- had decided to stay in the capital, while another wanted to head to the northern city of Bremen, Landshut officials said.
The refugees did not realise they were part of a stunt [AFP]
Both German news channel n-tv and Zeit newspaper's online edition said refugees on the bus did not know the trip had been organised as an act to criticise Merkel's immigration plan.
The refugees thought of the trip to the German capital as an opportunity and were upset when they found out they had been used by Landshut politicians to make a stance against the federal government, both outlets reported.
Guenther Burkhardt is the head of German refugee support group Pro Asyl.
He criticised the refugee road trip, saying "people are being exploited for the sake of media footage".
"This doesn't solve the problems... this is a stunt that misuses the plight of refugees to send the message 'We want to close the borders'."
'No end in sight'
While media and police stood around the bus, Berlin city officials boarded to negotiate with the Bavarian officials, as Syrians looked on with worried faces, glancing nervously at the TV cameras outside.
|There is no end in sight to the wave of refugees, and our country's ability to house them in a dignified way is deteriorating rapidly
- Landshut district councillor Peter Dreier
After two hours, Dreier said he had agreed to personally pay for the refugees' first night in a Berlin hotel, stressing that the bus had also been laid on by "a private person", not with taxpayer money.
He said some of the refugees wanted to later take a look at available Berlin accommodation, others had asked to travel on to another city, Hamburg, and whomever of the others wanted to return Landshut would be permitted.
"Let's get some rest and see tomorrow," said Dreier, of the small Free Voters party, while sporting a traditional Bavarian coat for his trip to the capital.
Merkel has been praised for opening Germany's doors to those fleeing war and misery, but has also weathered harsh criticism, especially from Bavaria state, the main gateway for arriving refugees and other migrants.
"There is no end in sight to the wave of refugees, and our country's ability to house them in a dignified way is deteriorating rapidly," said Dreier. "And I don't see new apartments being built for the immigrants."
He said his district had 66 migrant facilities, and around 70 more refugees were arriving each week.
Although the 31 Syrians had official asylum status and were now free to look for a home anywhere in Germany, he said he had been keeping them in shelters so they would not end up homeless.