The Black Caps scored 294-5 with Guptill hitting 102, before Sri Lanka were dismissed for 258.
Sri Lanka captain Angelo Mathews hit 95 in the fifth and final match of the series, but they lost their last five wickets for just 35 runs in six overs.
Matt Henry finished with 5-50 to give him 13 wickets in the series.
New Zealand captain Brendon McCullum, who announced last month he would retire from international cricket in February, was once again absent after suffering a back injury colliding with an advertising hoarding.
The hosts had also dominated the Test series to win 2-0.
New Zealand sealed a 3-1 one-day series win against Sri Lanka with a Martin Guptill century helping them to a 36-run victory at Mount Maunganui.