The Senegal striker, signed for £9.5million from Freiburg in January, slotted low beyond Michel Vorm after just five minutes at the Liberty Stadium, before a brilliant chip sealed the victory with 21 minutes remaining.
The goals gave Cisse a brace in each of his last three appearances, and he has now scored nine in his last eight games.
Pardew said: "We have a guy in red-hot form in Cisse and that was the difference between the sides. We weren't brilliant today, we were a bit flat, but he was electric.
"But his form doesn't surprise us, we see him in training every day.
"You need a bit of luck when you come into the Premier League, but he got a great first goal that has set him on the road in terms of confidence.
"He had a fantastic record in the Bundesliga with a club that were struggling, so he is no mystery. He is a player with pedigree.
"When you play Swansea you won't get 20 chances as they keep the ball so well, so the strikers have to keep their focus.
"They may get just one chance and he was focused on those two chances and did not let us down.
"His second goal, it was like a Masters golf shot.
"I thought it had gone over in mid-air but it had that bit of backspin on it. It was a terrific finish."