The 262-km 11th stage, the longest of the three-week race, was so inundated with rain that the peleton wore wet weather jackets to protect them from the foul weather which has dominated this year's extravaganza.
Nothing could stop a large breakaway group early on, however, and Astana's Vinokourov was stuck way down the field as new pink jersey holder Porte took up a position toward the front.
The unheralded Saxobank rider, who had been sixth overall, suddenly has a 1 minute 42 second race lead over Spain's David Arroyo of Caisse D'Epargne.
"It was a long, hard day. I had two teammates who annihilated themselves for me. It's thanks to the team," Porte, a Tasmanian like stage nine winner Matthew Goss, told Rai TV.
"This week Tasmania is showing itself to be the center of cycling in Australia." Kazakhstan's Vinokourov had led since stage seven but is remarkably now down in 12th spot almost 10 minutes adrift of Porte.
Russia's Evgueni Petrov of the Katusha team won the stage after pulling away late on and whipping off his slightly ironic sunglasses as he crossed the line in the rain.
"I'm really happy. I want to say hello to my wife. I did it, I did it," he screamed to reporters.
Petrov completed the route in six hours 28 minutes 29 seconds ahead of Dario Cataldo and Carlos Sastre.
The stage finished in the central Italian city of L'Aquila, devastated by a huge earthquake in April 2009, and passed through several villages which had also been hit.
Many charity events connected to the Giro are taking place to raise money for the area.
Thursday's 12th stage goes from Citta Sant'Angelo to Porto Recanati along Italy's east coast with two tough mountain stages due at the weekend.
The world's second biggest stage race, damaged by a succession of doping scandals in recent years, ends in Verona on May 30.
In Santa Cruz, California, American David Zabriskie captured the third stage of the Tour of California, edging out Michael Rogers in a close finish to grab the overall lead on Tuesday.
The 31-year-old Zabriskie won the 182 kilometer (113 mile) stage from San Francisco to Santa Cruz. He leads Rogers by four seconds overall.
"The final climb was long and hard," said Zabriskie, the American national time-trial champ. "We were just trying to hold off the chase group." Zabriskie has twice finished second in four previous races but has never won a stage.
Three-time defending Tour of California champ Levi Leipheimer was third, also in the same time as the top two finishers.
Former Tour de France winner Lance Armstrong, of the US, finished a distant 14th. Armstrong is 12th overall, 27 seconds back.
The top three finishers all began the third stage in a group of 20, trailing Aussie Brett Lancaster by 10 seconds.
"I screwed up the finish," said Leipheimer. "I knew about the final corner, but Dave got the jump on us. I closed the gap to Mick (Rogers), but it was just too short to the finish to do anything." Lancaster, of Shepparton, Victoria, fell to 36th place overall after finishing 51st in the stage.
The fourth stage of the eight-day race will be run from San Jose to Modesto.
