PSG drew first blood in the last-16 fixture at the Santiago Bernabéu through midfielder Adrien Rabiot but a penalty on the brink of half-time saw Cristiano Ronaldo level matters.
Ronaldo completed his brace in the second-half before Marcelo's late third, which left Emery lamenting an alleged handball from Real captain Sergio Ramos, that the former Sevilla boss feels could have changed the outcome of the fixture.
"The team played well," Emery said after the game, as quoted via Sky Sports. "They showed character. We deserved a better result but the referee did not help us.
"Their penalty was not very clear and there was a clear penalty for us for a handball by Ramos. The referee took decisions that damaged us."