Sri Lanka will now have to play World Cup qualifiers in Zimbabwe in June.
This meant that they lost the three-ODI series to New Zealand 2-0 with one match being washed out and the Dasun Shanaka-led side had lost the first match by a massive 198 runs.
Chasing 158 for victory in Hamilton, New Zealand overcame a wobbly start that saw them lose two wickets in the second over and got home with 103 balls to spare thanks to an unbeaten 86 by batsman Will Young and a 44* by Henry Nicholls.
Earlier, Sri Lanka had won the toss and chosen to bat but only Pathum Nissanka (57), skipper Dasun Shanaka (31) and Chamika Karunaratne (24) could make notable scores as the side was dismissed for 158 runs. Matt Henry, Henry Shipley and Daryl Mitchell bagged three wickets each for New Zealand.
India, being the hosts, and six other teams have booked their spots in the World Cup starting in October, with the West Indies occupying the final automatic qualification place in the Super League standings.
The 1996 world champions received five points following the abandoned second ODI rather than the 10 a win would have offered and were also docked a point for maintaining a slow over-rate during their 198-run defeat in the opener.
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Sri Lanka ended their CWCSL campaign on 81 points. They will now travel to Zimbabwe for the 10-team ICC Men's Cricket World Cup Qualifier in June and look to secure their place in the ICC World Cup 2023.
New Zealand, on the other hand, end on the top spot of the CWCSL standings, accumulating 175 points in their campaign.
(Reuters inputs)