Barnes, most recently the managing director of the digital company Oxigen, takes over from Lawrie Procter on 13 September.
Procter announced last month that he was leaving to become the managing director of the regional newspaper sales operation MarketForce.
Barnes, who spent 20 years at Associated Newspapers, left the publisher in 2000 after a falling out over the direction of its contract publishing division, Unique Solutions in Publishing, where he was the managing director.
Before joining Unique, in early 1999, Barnes had been the ad director of The Mail on Sunday and launched its contract division, Contract Mail.
The Independent is currently putting in place a new sales strategy to take advantage of the gains in circulation made since the launch of its compact format last September.
Terry Grote, the managing director of The Independent, said: "His (Barnes') period out of newspapers has undoubtedly seen him recharge his enthusiasm and gave us the confidence that he will be the ideal person to lead a great team during this exciting time at The Independent."