The 32-year-old Porte is only the second Australian to win the one week tour after Cadel Evans in both 2006 and 2011.
Yates had taken the overall lead Saturday but had only a 19-second lead on Porte ahead of the challenging 17.8km time trial.
Sunday's stage was won by Slovenia's Primoz Roglic ahead of Porte six seconds back in second and his teammate Tejay Van Garderen in third.
Porte ended top of the overall standings 21 seconds ahead of Yates in second, with Roglic's stage win lifting him to an impressive third overall.
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