Portsmouth looked certain to record an historic victory with minutes to go but Milan put themselves back in the game through a Ronaldinho free-kick eight minutes from time.
Johnson's foul on Ronaldinho led to the free-kick from which the Brazilian scored, but the full-back believes it should never have been given.
"In my opinion it was never a foul," the England defender told BBC Five Live.
"It's one of those things, I suppose. Ronaldinho can cause havoc when he's on those free-kicks, as he showed.
"Obviously we worked really hard during the week. We worked our socks off and the score was a bit unlucky for the boys.
"I'm pleased to be playing at the moment but obviously we haven't had as much luck as we would have liked."