The international friendly, part of both sides' preparations for Euro 2016, had to be moved from Brussels to Portugal following the terrorist attacks on the Belgium capital earlier this month.
Nani opened the scoring after 20 minutes before Cristiano Ronaldo netted late in the first half.
The occasion was marked by a minute's silence before the game, while the players also wore special warm up kits bearing the message, "In memory of all victims Brussels, 22.03.2016".
But while Wilmots said he could not speak for the mental state of every player, he did not feel it should have been a factor in his team's performance.
"I'm not in the minds of players, but I do not think the emotional context explains our poor start to the game," he was quoted as saying by L'Equipe.
"[When the game starts], the minute of silence and hymns are behind us."
Wilmots said his side's problems were more widespread than just the defence and slammed the collective defensive effort.
"The problem was not just our defenders," he said.
"We left running men in the middle, when we leave them running with the technical quality of our opponents tonight, we cannot defend properly.
"We defend and attack together, I have not seen enough collective work in the first half.
"There was a reaction, [from] my defence in particular and it was much better in the second."
