Yamamoto's appointment ended Indian hopes of a Formula One comeback this year for Narain Karthikeyan, the Williams test driver who raced for Jordan in 2005 and had been one of those under consideration.
Yamamoto replaces Dutchman Christijan Albers, whose contract was terminated due to a sponsorship problem, alongside German rookie Adrian Sutil.
With Super Aguri's experienced Takuma Sato, he will be the second Japanese on the starting grid.
The 25-year-old from Toyohashi started seven races for Honda-backed Super Aguri last year and started this season as that team's second test driver as well as racing in the GP2 support series.
"I am very pleased to get the opportunity to race in Formula One again," he said in a Spyker statement. "I know all the circuits we are going to very well, having raced at them with Aguri last year.
"I also know the team from my test in 2005 so I feel ready for the chance," added the Japanese, who made his Formula One debut with Spyker's predecessors Jordan as a test driver two years ago.
Spyker team principal Colin Kolles welcomed back Yamamoto, whose sponsorship backing will be a big help for a team that has yet to score a point.
"He is one of the most promising young Japanese drivers who showed potential in the races he contested in 2006 and I think he and Adrian will be a complementary pairing," he said.
"Sakon's experience of the circuits we visit in the second half of the season will be a big advantage to us as we move forward."
Honda's Austrian reserve driver Christian Klien was another who had been in the frame, testing for Spyker at Spa earlier this month, as was German Markus Winkelhock who raced for them in last weekend's European Grand Prix.
