With 30 September 2017 set as the cut-off date for automatic qualification, the Windies now cannot move ahead of Sri Lanka.
Jonny Bairstow scores maiden ODI century and Stokes took three for 43 ensured West Indies suffered a seven-wicket defeat at Old Trafford on Tuesday.
Visitors need to win the five-match ODI series by a margin of 5-0 or 4-0 for direct qualification for the 2019 global event.
MS Dhoni scored 79 runs and took 2 catches with a stumping, while Hardik Pandya blasted 83 and scalped 2 wickets.
Duo picked up six English batsmen as visitors defended 176 to win the one-off T20I after Gayle and Lewis set the agenda.
After won 9-0 in all format in Sri Lanka now face world champion and ODI no.1 team Australia.
The third and final Twenty20 International turned out to be a one-sided affair with Pakistan sealing a 33-run win over World XI at the Gaddafi Stadium on Friday
The India opener has asked for leave to look after his wife, who is unwell.
While Amla anchored the chase with a half-century, the series-levelling victory was made possible courtesy Thisara unbeaten 19-ball 47.
Ireland - West Indies one-off ODI at Stormont is abandoned after rain at lunchtime finally puts paid to hopes of any play.