Cisse 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 Senegalese forward was in dispute with Newcastle for some time over the club's shirt sponsor, Wonga, which is a payday loan company.
Cisse said the deal to wear the sponsor conflicted with his Muslim beliefs but after talks with his family and Islamic teachers, decided to drop his stance.
And in his first game wearing the shirt, the 28-year-old netted, making up for an earlier miss in the 19th minute with his goal.
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 Newcastle.
Sean Kelly had a great chance to head home a late consolation for St. Mirren but he headed over as Newcastle settled for a two-goal win in Scotland.
