England, which had started on 121 ratings points, slipped to 119 ratings points after the series loss, only to see India finish ahead of it by 0.2 when the ratings are calculated beyond the decimal point.
India had become the number-one ranked side after winning the third match of the series on January 19 and then held onto the spot thereafter.
England had gained the number-one spot in September 2012, while it is the second time since September 2009 that India has topped the current ranking system since it was introduced in 2002.
India's cause was also helped by South Africa, which lost to New Zealand 1-2. As a result, South Africa lost nine ratings points and dropped from second to fourth position, one ratings point behind third-ranked Australia.
New Zealand gained seven ratings points and moved ahead of Bangladesh into eighth position with 79 ratings points.
Meanwhile, Australia and Sri Lanka have retained their pre-series ODI ratings after their series ended in a two-all draw. Australia is now third at 113 ratings points while Sri Lanka is three ratings points behind in fifth spot.