Berry adjudged Walsall goalkeeper Sam Johnstone to have brought down Crewe winger Byron Moore in the area and Luke Murphy converted from the spot in the 78th minute before Chuks Aneke put the result beyond doubt with a superb finish four minutes from time.
Smith said: "There is no way it was a penalty and I'm disappointed that a poor refereeing decision has changed the outcome of the game.
"It's disappointing because we have had a great season and that has taken the wind out of sails right at the end.
"I thought we played really well on a really tough pitch and both teams tried to play.
"We had enough chances to score a few goals, but we didn't take them.
"It's been a great season and it's disappointing that it has finsihed this way, but I take great pride in the run we have had and what the players have given all season."
Crewe fielded a starting 11 made up entirely of academy products and Smith was full of admiration for the Gresty Road youth system.
"It's great what Crewe have done and all credit to them.
"Hopefully we can continue on a similar pathway and develop something like they have over the next few years."