The 27-year Senegal international claimed three points with his ninth goal of an indifferent season by his standards to complete a comeback which eased the Magpies into 13th place in the Premier League table.
Newcastle are now level on points with Fulham in 10th and, perhaps more importantly, nine clear of the relegation zone.
However, Cisse's strike two minutes into stoppage time came at the end of a game during which he had previously made little impact until his instincts took over.
Pardew said: "Papiss, I think, would be the first to tell you he was awful today.
"He didn't do anything, really, to influence other than doing well on some defensive issues for us.
"But then the moment comes. It's an eye-of-the-needle pass from [substitute Sylvain] Marveaux, which he has [in his game]. The ball pops up and most strikers would snatch at that.
"But he let it come all the way down and finished it and in the 92nd minute, that's not easy to do, trust me."
Newcastle were the better side on the day, but struggled to open Stoke up despite enjoying the lion's share of the possession, and they found themselves behind with just 23 minutes remaining.
Midfielder Cheick Tiote unceremoniously upended Jonathan Walters inside the penalty area and the Republic of Ireland striker, who has not enjoyed the best of fortunes from the spot this season, confidently blasted past keeper Rob Elliot.
But Newcastle were back in it within six minutes when, after Stoke midfielder Glenn Whelan had compounded a poor pass by tripping Moussa Sissoko on the edge of the box, Yohan Cabaye curled home an inch-perfect free-kick off the underside of the crossbar.
Stoke's misery was complete two minutes into added time when Cisse, who had early been involved in a bust-up with both Marc Wilson and Ryan Shawcross which City boss Tony Pulis believed might have earned him a red card, pounced to steer home Marveaux's through-ball and win the game.
Pardew said: "People get them mixed up sometimes, they talk about the spirit of the side and 'You must have a fantastic spirit to come back from a goal down'.
"You need world-class players. You need a world-class player to put that in the top corner from that free-kick to give you a foundation to win the game."