"I think the players gave 100% effort but with the problems we've had, we couldn't play any better," said Pfister.
The Togolese debutants suffered a turbulent build-up for the World Cup that witnessed players boycotting training after payment rows and Pfister quitting the team only days ahead of the tournament.
The German manager said that his team came to Germany as outsiders and managed to impress despite the early exit.
"We can't be happy but the team came here to learn and I think they put on a good show," he said.
Pfister also offered his congratulations to the Swiss, saying: "We can only congratulate the Swiss team because they won deservedly."
Switzerland coach Kobi Kuhn exchanged praise with Pfister's side, saying: "It wasn't easy against Togo. They had two very strong strikers and a midfield they pulled back."
Kuhn said that the win gives his team hope in qualifying for the second round.
"The 2-0 victory over Togo gives us more hope because we don't absolutely have to win our next match (against South Korea on Friday).
"The players knew that in the last minutes we needed to do everything to score another," he said.