Wigan had been looking to play the role of party poopers in West London, but were ripped apart as Chelsea secured a first Premier League title since 2006.
The Latics' task was made all the more difficult when Gary Caldwell was sent off with the score at 1-0 for pulling down Frank Lampard in the box, with the Blues midfielder scoring the resultant penalty.
Martinez admitted Caldwell's red card ruined his game-plan and he also felt there was an offside in the build-up to Nicolas Anelka's opening goal for the champions.
"It was a result that did not reflect what happened during the game," said Martinez.
"We all knew it was going to be a tough game, and unfortunately the first two big calls of the game went against us.
"They scored the first time they came anywhere near our goal, and it was clearly offside. Then we gave away a penalty, Gary Caldwell gets a red card, and it's very difficult after that.
"After that, it's a one-off game and it's extremely hard to adapt to the situation and get back into the game.
"You are always chasing it and, against a team that is fighting for the title, we were far too exposed at the back."
For the final game of the season, Martinez experimented with a three-man central defence and was satisfied with his team's performance up to Caldwell's dismissal.
He added: "We have played in different ways during the season, and it was an ideal scenario to adopt given the injuries we had and the way Chelsea play.
"I felt we were enjoying ourselves in the first half, but when you are reduced to 10 men and are chasing the game it makes all the preparation and all the plans pointless.
"It is a day to congratulate Chelsea and for ourselves to look back on a season of very many highs.
"I told the players before the game, we had won our league and achieved our aims - and that's what counts.
"We were determined not to come here and go through the motions, and it's clear we tried to do that and had a proper go.
"But when you go down to 10 men and you try to get back into it, you are going to leave yourselves exposed and you're playing into Chelsea's hands."