Bergara sustained a cut foot during a 2-0 Champions League defeat to Shakhtar Donetsk but coach Jagoba Arrasate is confident he will be fit in time.
Martinez has been out of action since injuring his thigh against Lyon on August 20 but was able to participate in a full training session during the week.
The potential return to the side of Zurutuza, who missed the clash with Shakhtar due to injury, is a huge boost to the Basque side, who are already without Gorka Elustondo and Esteban Granero, who has been ruled out of action for six months with damaged knee ligaments.
In a pre-match press conference, Arrasate hinted the club would look to bring in another midfielder to cover for Granero, but emphasised it would not be easy.
He said: "We signed Granero in the summer because we thought it was necessary [to bring in a midfielder] so now [we need another midfielder]. But it's complicated.
"We would have to exclude another player from the squad and our possibilities from the transfer market are scarce. We'll have a meeting and evaluate the situation."
Arrasate also asked the team to put the disappointment of their Champions League exploits behind them.
"It was a tough day, after the game the fans we're very frustrated with how the game panned out, but we have already talked about it and now we're thinking about Malaga," he added.
"Every three days we have a game and we cannot waste our energy on regrets. I'm more concerned about the game with Malaga than with our form."
On Bernd Schuster's side, he said: "They are similar to last season's team.
"They may have changed coach and a lot of players have left, but they are going in the same direction.
"They played well against Barcelona and Sevilla. We will give the best performance we can, and if we do that, we'll have a good chance of winning."
Malaga's only absentee for the match is centre-back and captain Weligton, who is still recovering from a fractured collarbone.
Midfielder Duda returns to the side after serving a suspension.