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The Sky star, who took possession of the leader's red jersey on Thursday, had a 27 second advantage over Spain's Contador in the overall standings with Australia's Evans 39s away in third.
Saturday's sixth and final stage, a 144km ride from Hawit Nagam park in the south of the emirate to Muscat along the Matrah corniche, was won by France's Nacer Bouhanni.
He finished clear in a sprint from Australia's Matthew Goss and USA rider Taylor Phinney.
"It's been an incredibly successful week for us this week. The team has rallied around me all the way and having guys of the calibre of Bradley Wiggins helping you to win a race makes it a hell of a lot easier to be up there when the going gets tough," said Froome.
"This is still very early days at the moment and early on in the season. This was a preparation event and a good test to see how the winter training has gone so far.
"I'm quite confident that I'm on track at the moment and right where I need to be with my preparations in view of being ready at 100 per cent for the Tour de France."