Cisse cursed as he left the pitch with the score at 0-0 and barely acknowledged his manager on the way to the dugout, where he continued to rant.
The 27-year-old was replaced by Shola Ameobi, who went on to score a vital winning goal that ended a run of only one victory in seven for Newcastle.
Afterwards, Cisse took to Twitter to express his regret at the outburst, tweeting: "Sometimes frustration is bad. I respect my manager and his decisions. Great win for the club and let's hope we can do the same in the next two big games."
Pardew was also keen to play down the incident, even praising Cisse's reaction to the disappointment of being taken off.
"Papiss just wants to play well," he said. "He loves Newcastle and the fans love him. That showed in his and their reaction when he was subbed. I have no problem with that. It's not a bad thing, it's a good thing."
Newcastle's fans appeared to side with Cisse on the matter by meeting his substitution with boos.
Pardew's decision was ultimately vindicated by Ameobi, but he nevertheless understands the supporters' feelings.
He added: "I think the boos were a nice moment for him [Cisse]. He seemed to walk off very slowly when he came off. You can't ask for more from our fans with the run we have been on. They have really showed their patience."
Cisse has struggled in his first full season at Newcastle, scoring only four times in his 22 appearances so far.
It has a been an alarming slump in form given that he netted 13 times in 14 matches last season after signing from Freiburg in the January transfer window.
Pardew, however, is in no doubt that Cisse can rediscover his goal-scoring touch.
"He knows he has the love of the fans on his side, although he has had a disappointing time," he added.
"But he is a goal-scorer. When you look at him in training, we are a little bit perplexed as to why he is not scoring goals. He had three good chances on Saturday.
"But I confidently predict Papiss will score more goals in the second half of the season."