During the 2-0 loss to Borussia Dortmund at Signal Iduna Park on Wednesday, Martinez attempted an acrobatic volley inside the Dortmund area, his swinging leg making contact with Marcel Schmelzer in awkward fashion.
The Spaniard was carried from the field on a stretcher after receiving treatment on his left knee and was replaced by Brazilian centre-back Dante.
Guardiola, who claimed to only have a handful of fully fit players before the game, was pessimistic in his assessment of the problem.
"The bad news is the injury to Javi Martinez," he said. "He was in good shape.
"We'll know what he's got tomorrow [Thursday]. But I think that he will be out for a long time."
Guardiola selected a mixture of first-team stars and inexperienced youngsters, with many players still recovering from a gruelling World Cup campaign with Germany.
One of those was Philipp Lahm, who was introduced at half-time for Thomas Muller, and the 30-year-old conceded it had been a tough task with so many regulars either unavailable or not at 100 per cent.
"We were missing a lot of players and we're still finding our feet in pre-season," he said. "It was difficult."
Robert Lewandowski made his return to Dortmund after leaving at the end of last season following four prolific campaigns at Signal Iduna Park.
Back at his former stomping ground, Lewandowski endured a miserable experience as he failed to make any impact on the game, watching on as his old club cruised to victory.
Goals in each half from Henrikh Mkhitaryan and Pierre-Emerick Aubameyang sealed the win for Jurgen Klopp's men, who made it successive Supercup successes over their rivals, after a 4-2 win in 2013.
"It was a tough game and we wanted to do better," said Lewandowski.
"It's hard to say why we didn't. I hope we can improve."
