It was a doubly disappointing result for Chelsea after they had hauled themselves back into the Barclays Premier League title race with victory over leaders Manchester City on Monday.
Manager Villas-Boas said: "They were two completely different halves. The first 20 minutes of the second half we were good and it was a question of patience until we found the goal. We could maybe have tried to go for the second goal but we decided to try to hold onto the first and exploit the space in behind. But we conceded two minutes from the end."
He added: "That is disappointing and prevented us from getting the three points that we had expected. It's a pity but the players fought hard and I think confidence is not affected."
After a first half short on chances, Daniel Sturridge broke the deadlock when he clinically converted Ashley Cole's pass for his ninth goal of the season.
Chelsea had a scare 14 minutes from time when a poor backpass from Branislav Ivanovic resulted in the defender having to clear a Franco Di Santo shot off the line, but they did not learn their lesson and Jordi Gomez tucked away an equaliser in the 88th minute.
The goal appeared to be avoidable, with Petr Cech failing to hold onto a poke towards goal from Hugo Rodallega, presenting the Spaniard with an empty net for his fourth goal in five matches. Villas-Boas did not single out his keeper for blame, though, adding: "It was collective mistakes. Wigan made the best of our lack of concentration."
Martinez, meanwhile, felt Wigan were harshly treated by referee Martin Atkinson, who turned down their penalty appeals after Victor Moses' shot had hit Ivanovic on the arm.
The Spaniard, who also disputed the addition of only four minutes of stoppage time, said: "I felt Ivanovic knew exactly what he was doing and he moved his body towards the ball. The arm was next to his body so I understand the referee's decision.
"Probably two or three big decisions did not go in our favour, but you expect Chelsea to have those moments. You need to be lucky to get a result against a team like Chelsea, and I don't think we were lucky at all."
Source: PA
Source: PA