The Republic of Ireland international was carried off on a stretcher in the first half of Tuesday's match against Kazakhstan and less than 24 hours later the club announced he would have to have an operation on his knee.
However, Martinez insists the 25-year-old's season is not over and he hopes the midfielder, who has been troubled by a number of injuries over the last 12 months, can return stronger.
"It was a real disappointment on Tuesday night," said the Spaniard.
"I was watching the game and straight away you could see it was an innocuous incident and that is normally when you pick up really bad injuries.
"I was really fearful of expecting the worst but with the scans on Wednesday we are very positive now.
"It is an ACL but the whole structure of the knee is perfectly fine and it is going to be straightforward surgery.
"I'm looking forward to seeing him back hopefully this season and that in a way was good, positive news taking into consideration what it could have been.
"The ACL is ruptured but his knee reacted really well and nothing else was damaged - in those sort of actions you normally get more than one structure damaged and some of those are very difficult to repair.
"You can imagine it is really disappointing to lose Darron for whatever space of time but we are all very positive that when he comes back he will come back stronger.
"We will use this period to get Darron working on other aspects of his fitness and making sure his knee is going to be perfectly repaired and ready for whenever he is back."
Martinez dismissed suggestions Gibson, who had played only 96 minutes for his club this season because of another knee problem, had been overworked on international duty.
The midfielder played all of the 3-0 defeat to Germany on Friday, his first competitive 90 minutes since the final game of last season, and was 37 minutes into the Kazakhstan match when the injury occurred.
"If it has been in the 80th minute then you can go down to detail and see if fatigue played a part in it," said Martinez.
"He looked really free in his movement and I thought the partnership he showed with (Everton team-mate) James McCarthy in the game was really exciting for everyone.
"When you watch it is so unfortunate the knee couldn't react any other way, so clearly it is one of those unexpected moments that you can't do anything about.
"I expected the worst and thought it would be a very difficult injury to overcome but now we are very positive and know Darron will be fully fit and recovered and will come back a stronger footballer at the end of it."
On the impact Gibson's loss will have on the squad Martinez added: "You don't want to lose players and in pre-season I felt Darron was magnificent.
"He brings something we haven't' got in the squad; his understanding on the ball and the way he was starting that partnership with James McCarthy was going to be important.
"But it is no good to look back, we are just looking forward and we want to see Darron fully fit as quickly as possible."