The win put Guyana Amazon Warriors on joint top with four points from three games.
The young turks are playing in the challenging English conditions with red duke ball for the first time in their career.
Maverick batsman Chris Gayle opted out of the ODI and T20 series against India citing personal reasons as the West Indies Cricket Board (WICB) named three fresh faces for the assignment.
Riding on scintillating centuries by Prithvi Shaw and Hanuma Vihari, India A scored a crushing 203-run victory over West Indies A to make the final of the Tri-Series one-day tournament, in Northampton, on Friday.
Captain Virat Kohli endured a rare failure but Rohit Sharma more than compensated with a blistering 162 to help India steamroll West Indies by 224 runs in the fourth ODI.
It was left to Shepherd to bowl Amazon Warriors' Super Over and he conceded just four runs to win the game for his team.
Left-arm spinner Ravindra Jadeja led India's brilliant bowling performance in a lopsided nine-wicket win against West Indies to wrap up a 3-1 series victory in the fifth and final one-day international.
Guyana Amazon Warriors crushed St. Lucia Zouks by seven wickets to jump to the second place in the points table.
Mohammed Nabi claimed five for 15 as he powered St. Lucia Zouks to a comprehensive six-wicket win over St Kitts & Nevis Patriots.
Khaleel Ahmed and Kuldeep Yadav picked up three wickets each after centuries from Rohit Sharma and Ambati Rayudu as India demolished West Indies by 224 runs, in the fourth ODI in Mumbai on Monday.
Captain Virat Kohli continued his record-breaking run with the bat but the rest of the Indian batsmen failed to live up to expectations as West Indies levelled the five match series 1-1 with a 43-run victory, in the third ODI in Pune.
Formidable India will hope to get more answers for their unsettled middle-order puzzle when they take on a reeling West Indies in the five-match ODI series, starting Sunday and ticking off the home team's countdown to the 2019 World Cup.
Images from the first ODI between India and the West Indies in Guwahati.
Who was the most valuable player of the India-West Indies ODI series?