First of all, Neymar also assisted Messi's goal, so that's a second possibility you conveniently left out. Second, Neymar was our main outlet, when you play possession football, this is what you need to kill the game off by either scoring another goal or running down the clock. By taking Neymar off, that outlet was no longer there, thus inviting pressure.
And that's no good when you have Iniesta and Rakitic having an off day and Xavi who is not a physical player in midfield. Enrique was to blame and he knows it. He could have left the same team for the last 15 min, or could have subbed off one of Iniesta, Rakitic or Suarez. Simple.