The German tactician was not pleased with the decision to send off Valon Behrami, but remains hopeful of making it to the last 16.
Just days earlier, the Swiss had pulled off a shock by defeating favorites Spain 1-0, but with 10 men they could not hold out on Monday versus the South Americans.
Switzerland coach Ottmar Hitzfeld admits that Chile made strides forward, but believes a place in the knock-out stages is still within his team's grasp.
"We played for 60 minutes with ten men against an active team like Chile," conceded the former Bayern Munich manager, according to AFP.
"It's very disappointing, but we can still get six points. It depends on us, we have to get three points against Honduras.
"We gave it everything we had, but it was annoying to concede a goal so late in the game."
Referee Khali Al Ghamdi sent off midfielder Valon Behrami during the first-half, and Hitzfeld seemingly does not agree with the decision. The official handed out nine yellow cards and one red during the course of the match.
"I think FIFA should make sure only the best referees are able to officiate at the World Cup," he concluded.
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