The Senegal Football Federation had wanted to include the 27-year-old among their squad for the tournament, which gets underway later this month.
However, having seen the former Freiburg frontman head off on African Nations Cup duty without kicking a ball following his £10million signing in January and with the prospect of having to do so again looming next season, the Magpies took the decision to keep him on Tyneside.
Cisse, who scored 13 goals for Newcastle as they surged into fifth place in the Barclays Premier League, reported for international duty once again at the end of last season as his country beat Liberia at home, but could only draw in Uganda.
Pardew said: "It was more the owners, really, who have to pay the guy's money.
"He had a full first half in Germany, he had the African Nations Cup, he had the second half of the season in his first year in the Premier League.
"He then had qualifying games, they want him again for the African Nations and they wanted him for the Olympics, and that was stretching it a little bit.
"As much as I feel for Papiss, because I am sure he would have wanted to play - he's not back yet, he's due back later this week - we have to make a call for his own health.
"I am sure he has got pressure from within the country for him to play and we have to release that pressure for him because physically, he couldn't do that. It's impossible."
Newcastle's caution with Cisse is perhaps understandable with strike-partner Demba Ba's future uncertain because of the release-clause in his contract and with Leon Best and Peter Lovenkrands having now left the club.
Pardew's hopes of adding FC Twente's Luuk de Jong to the mix were blown out of the water by the Dutch club's £16million valuation and as a result, the Senegal international's fitness or otherwise is a matter of huge importance.
Cisse will once again be a key figure as Pardew attempts to repeat last season's success while at the same time coping with the demands of Europa League football.
However, he is confident that, despite increasing optimism in the city, expectations will not be too high as they prepare to return to action.
Asked what owner Mike Ashley's targets for the new campaign are, the manager replied with a smile: "Mike's suggestion is we should win it, and with less money, so that's a bit tricky."
He added: "Look, we had a great season - I think our fans are realistic enough to know that we had a fabulous season last year.
"I met a lot of them on my travels on holiday, in the city or whatever, and they were all very pleased with last year.
"People keep telling me that their expectations are going to go through the roof and they are expecting us to improve or get the same.
"I don't see that. I think they are realistic enough to know that until a team breaks into the Champions League, it's very, very difficult to compete with those top four or five clubs.
"Obviously, that's what we are going to try to do, but it's difficult.
"When we consider we finished fifth, the next jump is considerable to get into that top four.
"We got to past Chelsea and Liverpool, which was a fantastic achievement, but we still didn't make the top four."
Pardew and those of his players who are back in harness will open their pre-season campaign in Germany tomorrow against Chemnitzer and will then face Monaco with a third fixture, against Fenerbahce, yet to be finalised as they attempt to re-arrange their programme following the cancellation of the Vodacom Challenge in South Africa.