The Senegalese was joined on the scoresheet by defender Mathieu Debuchy as the Premier League side controlled the match at St Mirren Park from start to finish.
The forward had been in dispute with Newcastle for some time over the club's shirt sponsor, payday loan company Wonga, which Cisse said conflicted with his Muslim beliefs but, after talks with his family and Islamic teachers, decided to drop his stance.
|40/1||Papiss Cisse is 40/1 with PaddyPower to be the Premier League's top goalscorer
Cisse began the move, passing to Sammy Ameobi on the left, and he continued his run, taking a touch after receiving the ball again before curling a superb strike into the top corner.
Dan Gosling had a header well saved shortly after but Newcastle doubled their advantage in the 26th minute.
French defender Debuchy was the scorer, getting in and behind the defence and converting Vurnon Anita's through-ball with a cool finish.
The match petered out in the second half with several substitutions made but 21-year-old Paul Dummett, who has been on loan at St Mirren twice, failed to convert one of his two late opportunities for the Magpies.
Sean Kelly had a great chance to head home a late consolation for the Scottish side but he headed over as Newcastle settled for a two-goal win.