Germany’s world time trial champion was always the favourite to win the final stage, and he did so with such ease that he was able to overhaul Sergio Henao, who had led after Saturday’s queen stage.
The 27-year-old adds this season's title to his 2011 win in Portugal. He was second last year.
"I am really happy," Martin said. "I was really looking to have a good day, and I had a good feeling immediately this morning during the reconnaissance.
"The parcour was really hard, with a lot of technical parts and little climbs where it was necessary to relaunch the action every time. Fortunately, it didn't rain during the TT.
"I really pushed a lot, and everything was perfect. There was a perfect approach to the race, and the result was because of all of these things."
Martin’s time of 45 minutes and nine seconds in the 35km ride from Castro Marim to Tavira was over a minute faster than OmegaPharma-QuickStep team-mate Michal Kwiatkowski, who was second on the day and overall.
Jesse Sergent of RadioShack was third in the time trial but only a second faster than Lieuwe Westra of Vacansoleil, who did enough to finish on the GC podium.
Colombia’s Henao was 3:15 off the pace and finished up in 12th.
Poland's Kwiatkowski, 22, was delighted with his first podium of the season.
"We did a great recon this morning with Tony and with him there is always something I can learn," Kwiatkowski said.
"Today I liked this kind of parcour. It was not one for the big gear - it was a bit more technical with a lot of shifting.
"I am very happy about the entire week, even on the climb yesterday. I saw the job I did in the last month to improve on the climbs pay off. I had good results at this race and I am happy about it."
Click on links for full results
1. Tony Martin (Ger) OmegaPharma-Quick-Step 45:09
2. Michal Kwiatkowski (Pol) OmegaPharma-Quick-Step +1.07
3. Jesse Sergent (NZ) RadioShack-Leopard +1.15
1. Martin 15:36.26
2. Kwiatkowski +58s
3. Lieuwe Westra (Ned) Vacansoleil-DCM +59