Everton took a 50th-minute lead at Craven Cottage when Fulham goalkeeper David Stockdale unwittingly diverted a deflected volley from Naismith into the net for an own goal.
Ashkan Dejagah came off the bench to score a stunning equaliser for Fulham in the 71st minute, cutting inside from the left flank and letting fly with a rising shot that flew into the top-left corner.
Mirallas restored Everton's lead eight minutes later, though, running onto a pass from fellow substitute Aiden McGeady and coolly beating Stockdale, before Naismith stabbed home the visitors' third in the 87th minute.
"The fresh legs of the subs were the reason we got the three points -- they gave us the spark to score the three goals," said Everton manager Martinez.
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"We would love to win the league, but we have got our targets and it is an exciting end to the season and we are fighting to be as high in the table as we can."
Fulham's chances of avoiding relegation appear increasingly remote, meanwhile, as they remain five points adrift of safety with only six matches to play.
"We have six games left. I still believe we can stay up."
Later on Sunday, Liverpool will look to exploit Chelsea's shock 1-0 loss at Crystal Palace on Saturday by beating Tottenham Hotspur at Anfield and taking over from Jose Mourinho's side at the top of the table.
Liverpool trail Chelsea by a point, while Manchester City are a point further back, albeit with two games in hand, after squandering a chance to go top in a 1-1 draw at Arsenal on Saturday.