Video footage has emerged of the team boss slamming the desk, his chair and angrily shouting at Mercedes chairman Niki Lauda at the moment Bottas swept past his British teammate.
Wolff admitted that switching the drivers while Hamilton is fighting for the world championship was one of the toughest decisions since he has been in charge of Mercedes.
"Sometimes doing it the right way and standing by your values is fucking tough, believe me. I feel crap," he said.
As for the video evidence that watching the outcome of his decision actually made Wolff lose his temper, a team spokesman said: "No.
"It was simply the release in tension as they crossed the finish line. The guys were really happy with the position swap."
The spokesman told Auto Bild that any confusion was because the swap of positions was not seen by those in the Mercedes pits live.
"So we had to look at the timing monitor. When it was over, Toto called out but it was a very exciting situation and certainly there was no anger about the outcome. On the contrary," he added.
Mercedes have a 39-point lead over Ferrari heading into the summer break.