Suarez's men were comprehensively beaten by France, slumping to a 3-0 loss in their Group E opener in Porto Alegre, but much talk after the match surrounded captain Noel Valladares' own goal in the second half.
A left-footed shot from Karim Benzema hit the inside of the post before striking Honduras goalkeeper Valladares, who attempted to prevent the ball from crossing the line but saw the Frenchman run away in celebration as referee Sandro Ricci awarded a goal.
As Honduras players protested the decision, goal-line technology deemed Benzema's initial shot had not crossed the line, sparking confusion on the sidelines. However, a second replay showed the ball had subsequently gone in off Valladares, proving Ricci's decision to be correct.
"I wasn't upset because it was a goal. I was upset because the technology first declared that it wasn't a goal, then it was a goal," said Suarez after the match.
"I don't know which one I should believe. If technology should make everything clear, why at the beginning did the blessed machine say no and then yes... what is the truth?"
It was a forgettable night for Honduras, who also had midfielder Wilson Palacios sent off in the first half for a second bookable offence.
Yet Suarez believes talk about Honduras' aggressive style of play in the lead-up to Sunday's match may have conspired against his team.
"I look for a way to play with an intense style but respecting the rules," said Suarez, who was forced to repeatedly defend his country's physical approach prior to kick-off.
"If we erred in terms of the rules, the referees are there to impart justice. If we made a mistake, well they would give us a red card as they did today and we have to accept that.
"During all this time, this is the first time we have seen a red card. Afterwards, and I hope this doesn't sound like I am whining, regarding what I said before about the way it was handled - saying what was said about Honduras, it could be interpreted in a certain way in certain situations."
Honduras will seek to bounce back when they take on Ecuador in Curitiba on Friday, before rounding off their group campaign against Switzerland the following Wednesday.
