Messi guided in a superb first-half free-kick to secure a 1-0 victory over Barca's nearest title rival, moving the league leader eight points clear at the top.
It was his 600th career goal and marked a major moment in the Blaugrana's bid to win LaLiga.
Simeone claimed the Camp Nou result would have been reversed had Messi been on his side.
"Messi is a special player, he made the difference," Simeone said. "If we take Messi and put him in an Atletico shirt, we win this match 1-0.
"It was an even match. I don't think we lacked application in the first half. However, we did not see our best until the second half."
Despite being dealt just a second defeat in its 27 league games this term, the Rojiblancos now have only a remote chance of claiming what would be a second title triumph in five seasons.
Simeone was pragmatic about his club's hopes of regularly upsetting the Barca-Real Madrid stronghold.
"We have no doubt that we can get closer to our objectives," he said. "What we cannot do is distance ourselves from the numerical reality that Barcelona and Real Madrid have been dominating for 14 years.
"We did the impossible [in 2013-14] and it is hard to repeat that."