Fifa intervened on Sunday to persuade Togo's players not to boycott their World Cup game with Switzerland.
The squad finally boarded their bus to Dortmund where the Hawks will play their second Group G match against Switzerland on Monday.
The players had initially stayed in their Wangen base while they discussed a long-running pay dispute.
"As far as we understand the team did not want to play," a Fifa spokesman said.
"The Fifa delegate there told them it would be extremely serious. He told them to be reasonable and they were," the spokesman said.
No team that has qualified for a World Cup finals has withdrawn from a match in the 76-year history of the event.
Any nation doing so face a heavy fine and could be banned from subsequent competitions.
"We are on the bus now," coach Otto Pfister said.
"I think they have found a solution but I don't know what it is and I don't want to know," he added.
The team will catch a flight from Friedrichshafen airport.
The Togolese, beaten 2-1 by South Korea in their opening match on their World Cup debut, did not leave their base in Wangen on Sunday in time to catch their scheduled morning flight to Dortmund.
Instead players held crisis meetings with officials over the pay row.
The dispute had prompted Pfister, a German, to walk out just before the tournament, saying it made it impossible for him to do his job.
He returned just in time for the first match.
Players from the tiny West African country have demanded US$196,300 each to play and US$38,000 for each win, half that for each draw.
But officials from the country with an average per capita income of well below US$1,000 have said those demands are too high.
Anyone else hear about it on last nights commentry between France and S.Korea? Disgrace