The Manchester City captain was sent off inside the first 10 minutes against Hull but his side still battled to a 2-0 victory at the KC Stadium.
Kompany was given his marching orders in the 10th minute after he hauled down a goal-bound Nikica Jelavic at the KC Stadium.
The visitors shrugged off the setback to win 2-0 courtesy of David Silva's stunning first-half effort and Edin Dzeko's last-minute strike.
Pellegrini conceded that Kompany's foul on Jelavic was worthy of a dismissal but he felt that the Hull striker should have been punished prior to that.
"It is clear that before Vincent's foul there is a foul from Jelavic that the referee didn’t see and didn't whistle for," the manager said. "Of course Vincent's foul is a red card, but there was a foul from Jelavic before."
The result provided the visitors with the perfect tonic following a week of woe that saw them dumped out of the FA Cup and Champions League in the space of four days.
"We won the game and we played very well — it was a very good response in a very difficult week," Pellegrini added. "We just lost against Wigan and against Barcelona and we needed to win today. Playing with one player less was very difficult.
"It was a good performance because we defended well with the ball and without the ball, and we also had three good chances to score. It was a very professional response from the players."