The prolific Martinez has been ruled out of the second leg of the last 16 tie after suffering a torn thigh muscle in Friday's 1-0 Primeira Liga victory at Braga.
Adrian Lopez (thigh) will also miss the out against the Swiss champions, but Oliver Torres (shoulder) is back in the squad.
The 1-1 draw at Basel came in between two three-game winning runs, during which Martinez scored three times to take his tally to 25 goals in all competitions this season - but Lopetegui will have to contend with his absence this time around.
"We are talking about the quarter-finals of the Champions League, of the opportunity to be among the best eight of the competition," the coach said.
"We're tied and Basel will ensure we are at our best to go through. We have to overcome an opponent that has had a great campaign in the Champions League and has been doing well in Europe in the past two seasons as well.
"We have to be able to cope with our injuries, it has to be accepted. We started this journey without a ticket [qualifying for the group phase via the play-offs], we had to earn it and now we are here."
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