The 27-year-old Team Sky cyclist – the Olympic time-trial bronze medalist and second in last year's Tour de France – had 54 seconds to spare over second-placed Slovenian Simon Spilak while Portugal's Rui Costa filled third spot just as he did last year.
Germany's time-trial specialist Tony Martin displayed his expertise in the discipline by winning Sunday's final stage in Geneva.
Froome, already winner this season of the Tour of Oman and the International Criterium, will hope he goes on and replicates the Tour de France success of the past two winners of this race, Australia's Cadel Evans in 2011 and the Briton's compatriot and Sky team-mate Bradley Wiggins last year.
Froome, born in South Africa and brought up in Kenya, said it was a good sign for his Tour de France bid but added there was still work to do.
"It has been a really good week for us I am really happy with my condition now in the build-up to the Tour de France," said Froome.
"This week I couldn't have done it without the help of a really strong team around me.
"Every day since the prologue, they have protected me and kept me at the front of the race. I owe it to them this week.
"Every race I do now is a good test for me, to see exactly where my condition is and what I need to work on. It has been a really good experience for me this week.
"It is definitely a good omen, but the Tour is still two months away and I need to do a lot of hard training before then."