Mahan's fellow American Nick Watney made a 25 foot eagle putt on the first to reach nine under par at Doral.
And Rory McIlroy was only one behind when he two-putted the same green for birdie.
Mahan started with birdies at the first and third to regain top position on the 11 under, but Watney kept the pressure on with a further gain at the second.
McIlroy dropped back to six under, but Italy's Francesco Molinari and World Number One Martin Kaymer kept the European challenge burning by reaching nine under after three and two holes respectively.
World Number Three Luke Donald and Scot Martin Laird were among the group on eight under.
There was a two shot swing at the sixth as Watney bogeyed and Mahan advanced to 12 under.
That left Molinari – who captured his first WGC crown at last season’s HSBC Champions in Shanghai – alone in second on ten under.
Watney was joined in third by Laird, three-time Major Champion Padraig Harrington and WGC-Accenture Match Play winner Donald.