The Latics came from two-goals behind to record a vital victory at the DW Stadium which saw the Hammers crash out of the Premier League
A brace from Demba Ba looked to have given West Ham hope of survival, however after Charles N'Zogbia got a goal back for the Latics, Conor Sammon equalised before N'Zogbia secured a priceless 3-2 victory in stoppage time.
"I feel the players were magnificent today," Martinez told reporters after the match.
"I feel that was a better performance than the one against Arsenal [last season]. The importance of the three points and probably our first half reflected that."
The Latics boss conceded that the Hammers made the better start to match - and subsequently stormed into a two-goal lead - but was delighted with his side's response.
"We couldn't hold the ball or effect the game too much. West Ham, I felt, started really, really well. They prepared the game in a really good manner," he continued.
"Then when you concede to the first attack you were defending. At half-time, it was a real, real mountain for us but that's when the character comes out.
"I was really proud and I said that to the players. I don't think the second 45 minutes was an accident, it was the work we have put in during the last 10 months."
The Wigan boss rang the changes at half-time, and admitted that his side had to take a risk as they were on the verge of the drop.
"It was the situation we were in," said Martinez. "We've got many, many options and we had to use them."
"We had to take risks. 2-0 down and you are relegated. In that moment we had to make sure we use our squad well.
"It's not just me making the changes, the players had to come on with the right mental attitude and approach to effect the game.
"If you look at the performances of Conor Sammon and Victor Moses, they really sparkled the team performance.
"[In the last 15 minutes] It was like rolling the years back. Today's game was something unique.
"It was a unique moment in our history and I hope that we can prepare properly for Sunday and face the second 'final' we have got."