Rayudu, who was drafted in place of an injured Rohit Sharma, stitched 87 runs with Suresh Raina (42) from 14.5 overs for the fourth wicket as India chased down the modest target of 228 with 42 balls to spare.
Ajinkya Rahane, who was promoted to opener's slot, made 45 while Virat Kohli struck 40, his highest innings score of the tour so far, as Indian batsmen had an easy outing against a pedestrian-looking England bowlers at Trent Bridge.
Rayudu grabbed his chance of making it to the playing eleven with both hands as he scored his third half century in his 14th ODI. He hit six fours in his 78-ball unbeaten knock.
Rayudu himself struck the winning runs -- a two off James Tredwell as India reached 228 for four in 43 overs to fashion a clinical win to the celebration of the Indians at the dressing room and seizable supporters at the stand.
Ravindra Jadeja was the other unbeaten batsman on 12.
The visiting batsmen played sensible cricket without taking much risks after their bowlers, led by off-spinner Ravichandran Ashwin (3/39), had put them on top by dismissing England for 227.
Shikhar Dhawan was the lone Indian batsman who did not make a substantial contribution in the match which saw home side paceman James Anderson being booed by Indian supporters.
Anderson was involved in an ugly spat with Indian all-rounder Ravindra Jadeja in the first Test at the same venue here. India had lost the five-match Test series 1-3.
The first ODI at Bristol was abandoned without a ball being bowled due to rains. The remaining two ODIs of the series will be played at Birmingham (Sept 2) and Leeds (Sept 5).