Martin wins as Contador flops in Algarve
The HTC-Highroad rider hammered through the 17.2km course from Lagoa to Portimao in 20 minutes 53 seconds to take overall victory ahead of team-mate Tejay Van Garderen.
Contador, who was defending his title, had been in second place since Thursday but dropped to fourth after finishing the time trial 45 seconds slower than Martin.
Vacansoleil's Lieuwe Westra was the only rider to get within striking distance of the German in the time trial, finishing five seconds behind to take third place overall. RadioShack's Tiago Machado was third on the final stage, 26 seconds behind Martin.
"It all went really well," HTC-Highroad sports director Brian Holm said.
"The course was pretty tough, a few tricky corners, but when Tony's in the kind of form he's got right now, to be honest, that didn't matter much, they could have thrown anything at him and he'll still have done well."
Britain's Stephen Cummings (Team Sky) had a disappointing final day, losing his overnight lead as he finished over a minute off the pace to drop down to seventh in the general classification.