Porte, who had trailed Contador by 22 seconds at the start of the 10th stage, dropped out of the top three in the overall standings after losing 47 seconds on the Spaniard.
Boem pipped fellow Italian Matteo Busato to the finish line to win the stage in four hours 26 minutes and 16 seconds.
"I'm really, really happy. Of course, it was unexpected to win today as it was the easiest stage but 20 kilometres to go I had a really good advantage... I could not let the opportunity go," Boem told Eurosport.
Former Tour de France champion Contador maintained his three second lead over Astana rider Fabio Aru in the overall standings. Spaniard Mikel Landa, also from Astana, climbed to third while fourth-placed Porte trails the pace-setter by one minute nine seconds.
"It's never an easy day, seeing Richie Porte's case, nothing ever goes to plan. I've had my bad moment and Richie's had his bad moment today," said Tinkoff-Saxo rider Contador, who dislocated his shoulder following a high speed pile-up during last week's sixth stage.
(Writing by Pritha Sarkar, editing by Ed Osmond)
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