The £15 million waterfront scheme will become the architect's second major cultural project in the UK, having already scooped the contest for the Hepworth Gallery in Wakefield.
Chipperfield, who is best known in Britain for his Stirling-nominated River and Rowing Museum at Henley-on-Thames, saw off an impressive shortlist to land the 'landmark gallery' development.
The other finalists were Allford Hall Monaghan Morris, locally-based CTM Architects, John McAslan and Partners, Patel Taylor and Danish hotshots Schmidt, Hammer and Lassen.
Kent County Council's decision to appoint Chipperfield comes less than six months after the authority pulled the plug on an ambitious pebble-shaped scheme by Snohetta and Spence because of spiralling costs (see AJ 08.02.06).
According to reports, the budget for the original art gallery, which was intended to sit in the sea off Margate pier, had ballooned from £7 million to almost £50 million.
Following today's announcement Chipperfield will now work with Arts Council England, the South East England Development Agency, Tate, Thanet District Council, and the Turner Contemporary Development Trust to draw up designs for the centre which is now intended to be built on a former car-park site.
Speaking about the competition judging, Tate director Nicholas Serota, said: 'We were faced with a strong field from which to select and I am delighted that David Chipperfield Architects has been chosen.'
The Arts Council's South East executive director Felicity Harvest added: 'Turner Contemporary has already established a strong regional presence through its extensive education and community outreach programmes over the last five years. This exciting new space will provide a base to develop this further, as well as extending JMW Turner's revolutionary vision to inspire new generations of contemporary artists.'
The new building, which will house a range of facilities, is expected to open its doors to the public in 2009.