The Belgium international suffered a small tear in his groin against Manchester United on Sunday but is expected to be fit in time for the World Cup in Brazil
The Belgium international was substituted in stoppage time during Everton's 2-0 win over Manchester United on Sunday after sustaining the problem, having scored his side's second goal just before half-time.
"Kevin's scans came back and they have revealed a small tear in his groin," Martinez told the club's official website.
"He is going to be out for the season which is a real disappointment and a shame because he was in a phenomenal moment of form
"But the memory we have of his performance against Manchester United is a terrific image. The way he took his goal and how he dynamic force throughout the game – it was an outstanding performance.
"It’s a great way to finish the season if it’s the last game he is going to be involved in this campaign."
Mirallas is expected to be part of Belgium's World Cup squad, although this injury means he faces a race against time to be fully fit.
"It is not a major injury. It could be anything up to five or six weeks, and that’s looking at the worst-case scenario. Kevin is a quick healer and I would be surprised if he is not available after three or four weeks," he added.
"It’s a shame because we had three really important games and Kevin has always been really influential this campaign.
"But the most important aspect now is that we get him fully fit and ready to participate with Belgium in the World Cup."