The match in Kanpur, had to be decided by the Duckworth/Lewis method after bad light stopped played.
Coventrian Ian Bell made 46 for England with fellow opener Ravi Bopara top scoring with sixty.
Owawi Shah added forty with Flintoff and Patel both hitting 26 in an England total of 240 all out.
In reply, India were 198-5 with Flintoff taking 3-31 before bad light stopped played and the home side given a sixteen run victory