The duo helped Sri Lanka post a challenging 216 for seven in 50 overs.
Sri Lankan fast bowlers Malinga and Kulasekara were bang on target right from the start and New Zealand failed to recover from a poor start. Grant Elliot offered some resistance with his patient 41 while fast bowler Ian Butler scored 25.
Earlier in the day, the 32-year-old Samaraweera smashed 10 fours in his 124-ball innings as he became the oldest Sri Lankan to score a maiden one-day hundred.
New Zealand fast bowler Shane Bond made an impressive return to one-day cricket with his 3-43 off 10 overs. The fast bowler was playing his first ODI after two years and didn't allow the Sri Lankans a good start.