The Senegal Football Federation had wanted to include the 27-year-old among their squad for the tournament, which gets underway later this month.
"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," Pardew said.
Having seen the former Freiburg frontman head off on African Nations Cup duty without kicking a ball following his £10 million 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 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."
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 £16m valuation and as a result, the Senegal international's fitness or otherwise is a matter of huge importance.