Everton took the lead in the first half through Leon Osman only for Fulham to gain the upper hand after the break and equalise through Dimitar Berbatov from the penalty spot.
The home side hit back with three quick goals late on, as Seamus Coleman, Gareth Barry and Kevin Mirallas all found the target.
And speaking to Sky Sports after the game, Martinez was delighted with the way his team turned things around.
Martinez said: "It was a really difficult game and the big moment was the penalty.
"After they scored we were more open-minded and it is great to score in games like this.
"Fulham were good and pressed with plenty of energy but we found a way to win and we have three very important points."
Martinez also had words of praise for opposite number Rene Meulensteen and thought his Fulham side might count themselves unlucky.
Martinez added: "Rene has got them going and they all know what they are fighting for but today their goal changed our mindset.
"I am not sure how far we can go but I have the perfect blend of players and when we find that consistency I expect us to do well."