Cisse failed to hit the target from the spot and Pardew explained that the Senegal international had been allowed to take the kick by his team-mates in an attempt to boost his confidence in front of goal.
After a prolific start to his career on Tyneside, the goals have dried up for Cisse this season and the former West Ham manager explained that the striker is not at the top of his usual list of penalty takers.
"I just wanted my penalty taker to take it, that would be a start! But I can understand the group wanting to give it to Papiss," Pardew told reporters. "It says a lot about the spirit in the group that they wanted him to score, but it wasn't what I wanted.
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"I can understand why they did that, they want Papiss to score and players do that, players want players to score and you'd be surprised, it's not as cut throat as the media put out. They genuinely wanted him to score the goal, the fact that he missed it was a blow to the group and we felt it in the dressing room.
"I expected Hatem [Ben Arfa] or Demba to take it, when players are playing well, they grab the ball. I've never been too fussed really, but today I thought it was the wrong player at the wrong time."
Pardew was pleased, however, with his team's ability to grind out results despite a run of performances which he acknowledged had not been of the "champagne" variety.
"We got nervous and we got a bit deep and I thought we lacked a bit of ambition in the second half," he conceded. "I can't help feeling the penalty miss had something to do with that. If we'd been 2-0 up, I think we would have seen the game out a little bit more comfortably.
"But I can't fault the players, we've had a really tough run of games, we've not put in any kind of champagne performance anywhere along the line here but we've kind of ground results out like we did today, and that's a good sign really."
Norwich manager Chris Hughton insisted that he was happy his team's performance despite their defeat but admitted that the Canaries were wasteful in front of goal.
The loss comes off the back of draws against QPR, Tottenham and West Ham in which Norwich were left feeling aggrieved at having not taken more points.
"We're on the back of four good performances," Hughton said. "Having been here [as manager] I know how tough it is to get a result. It wasn't one of Newcastle's better performances but it's tough to get something here, so if we can show that performance again, we can get that win.
"You make your own luck, but we haven't had a lucky penalty, or a deflected goal. We haven't had that little bit of fortune, but you make that yourself. I'd like to think the players will come away, learn what didn't give us what we wanted and put things right."
The 53-year-old received a warm reception on his return to Tyneside, where he managed for two years and masterminded the Magpies' return to the Premier League.
"It was always one I was looking forward to, the reception was excellent, and I'm delighted with that," Hughton commented. "I wanted a better day, and us to get a result that on the balance of play we probably deserved."