Despite the Brazilian's missed spot-kick, Barcelona claimed a 3-1 win over Villarreal in their Copa del Rey semi-final first leg.
Luis Enrique said Neymar must have decided with Messi to take the penalty, but had no doubts the Argentina international was still his main man from the spot.
"Normally, Leo is the guy who shoots the penalties. Neymar is the second in the list. After, the players have the main role," he told a media conference.
"I don't know how it happened. I guess, Ney asked the permission to shoot the penalty and they are who have the final decision.
"I really believe, as a player I was, it's very important the feeling of each player. If they trust themselves and they talk each other I give them all the credit.
"They are both of them the first choices in the list, but you know that Leo is the guy who is in the top."
Manu Trigueros had cancelled out Messi's first-half goal, but strikes after the break from Andres Iniesta and Gerard Pique saw Barca take a huge step towards the final.
Luis Enrique said Barca would still head to the Estadio El Madrigal looking for a win.
"Overall we had a good performance against a team which was more defensive than we expected, but brilliant team at the end of the day," he said.
"The score is good but it’s not decisive. It could be better if we wouldn’t have miss the penalty but it’s nice score.
"In my opinion it’s not totally fair, but overall it’s a good result and it doesn’t change our mentality. We are going to attack at Madrigal. Our aim is to win in the second leg, that’s our plan."
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