The highly-regarded 23-year-old, who is a member of the Ferrari driver academy, is currently in his rookie season with a best result of 13th in Malaysia.
The British-based team will swap Cosworth engines for Ferrari power units next year, when the rules go through major changes and a new turbocharged V6 is introduced, but principal John Booth said the deals were not linked.
"There is a link of course, because Jules is a Ferrari driver, but there's no link in the deal whatsoever," he told Reuters at the Korean Grand Prix. "It's a nice fit."
Marussia are currently 10th of the 11 teams in the constructors' standings despite having so far failed to score a point since their debut in 2010 as Virgin Racing.
The Frenchman secured the Marussia drive this year at the last minute after losing out to Germany's Adrian Sutil for a place at Force India.
With that door closed to him, another opened when Marussia terminated the contract of Brazilian Luiz Razia when his financial backing failed to materialise.
"Jules joined us at very short notice at the end of pre-season testing, with only two days of running under his belt," said Booth in announcing the contract extension.
"He rose to the challenge of his debut season exceptionally well and since that time has clearly demonstrated his ability and potential."
Britain's Max Chilton is currently Bianchi's team-mate and Booth said Marussia were talking with him about an extension.
"I have always made it plain I'd love to run the same drivers next year," he said. "So we've got half the job done."
Booth said the team had announced Bianchi's deal without waiting for the full line-up because such news inevitably leaked out anyway.
"There's nothing to be read into Max's situation at all," added the principal.
Chilton, who has brought funding to Marussia this year, told reporters he was not talking to any other teams and wanted to stay.
"The team are obviously keen to sign both of us, we're just not at the same stage as Jules was... we're working on things and progressing nicely," he said.
Asked how confident he was of remaining, he replied: "You never know in Formula One. The option's there, it's just whether I can get everything together. It's not as simple as it sometimes looks.
"I believe I've proven I deserve a chance and it's just trying to get the deal done."