Islands In The Stream, which features guest vocals from Tom Jones, is the 11th Comic Relief single to top the charts.
It adds to the £5.5m already raised by Comic Relief songs over the past two decades.
This week’s number two single, Just Can’t Get Enough by girl band The Saturdays, is also in aid of the charity.
Comic Relief 2009 raised a record £57.8m during Friday night’s star-studded telethon, with another £20m worth of donations expected to flood in.
In other chart news, the first American Idol winner Kelly Clarkson had a new entry in the album chart at number three with her latest effort All I Ever Wanted.