Martinez's sixth-placed side were left to dwell on a third straight away defeat in the Premier League when Chelsea struck at the death on Saturday.
A Frank Lampard set-piece from the left found its way into the net via a touch off home captain John Terry, who applied pressure to Everton goalkeeper Tim Howard and was ultimately credited with the goal.
However, Martinez felt the free-kick from which Chelsea scored should never have been awarded, believing referee Lee Probert was placed in a difficult position when Ramires tumbled under a challenge from Phil Jagielka.
Acknowledging Chelsea's stunning unbeaten home league run under Mourinho, which now stands at 74 games, Martinez pointed to the London club's ability to win free-kicks in key positions but stopped short of condemning what he described as "incredible know-how".
"Ramires looks for the contact and, if you watch the replay, it’s not a free-kick at all," said the Spaniard.
"But that happened with other incidents, four or five before that, and I don’t blame the referee at all. It's impossible to get the correct calls because you need a magic ball.
"I think you saw today why Chelsea are 73, 74 games unbeaten at home. I think it's an incredible know-how, using every single trick in the book to try to get advantageous positions.
"That happens everywhere. Just look at the record that Chelsea has at home (and) they must be more than playing well every week."
Everton delivered an impressive display in defeat and Martinez was understandably frustrated by their lack of reward.
"The scoreline is what matters in the short-term and we are hurt, we're not going to hide it, but the performance is exactly what we needed," he added.
"We showed that we can play eye-to-eye with the league leaders.
"We need to make sure that when we deserve to get a positive result, we do that. But I'm excited about what's ahead of us. I thought we were magnificent.
"Tim Howard had a period of 5-10 minutes that he was at his best (in the second half) but from that point on I couldn't see Chelsea scoring from open play."