The Argentine forward scored a wonderful free-kick in the first half which proved to be the difference between the two teams.
"If we take Messi and put him in an Atletico shirt, we win this match 1-0," Simeone explained in his post-match press conference.
"We have no doubt that we can get closer to our objectives.
"What we can't do is distance ourselves from the numerical reality that Barcelona and Real Madrid have been dominating for 14 years, we did the impossible [in winning the 2013/14 title] and it's hard to repeat that."
The match itself was billed as a LaLiga decider yet it lacked the usual spark of a heavyweight clash, the former River Plate coach however believes it was a very even encounter.
"It was an even match, I don't think we lacked application in the first half," Simeone admitted. "However, we didn't see our best until the second half.
"Messi is a special player, he made the difference."