Grant Elliott took 4-22 as New Zealand restricted Sri Lanka to 142-8 batting first.
Guptill then reached his 50 off 19 balls and Munro needed just 14 deliveries, hitting a six on the last ball of the tenth over to end the lopsided contest, with New Zealand finishing on 147-1.
Munro's half century, which included seven sixes, was the second-fastest in all T20 internationals, behind only a 12-ball 50 by India's Yuvraj Singh.
Sri Lanka beat Zimbabwe by 7 wickets in 2nd ODI