Silverbacks coach Eric Wynalda took almost as many shots at a ref — not the one you’d think — after the game as his team did against Chicago in Wednesday’s 3-1 loss in the quarterfinals of the Lamar Hunt U.S. Open Cup.

Though the Silverbacks outplayed Chicago for most of the game’s first 80 minutes, the result turned on a penalty kick that Chicago’s Jeff Larentowicz converted in the 82nd minute. Silverbacks defender Mike Randolph was judged to have tripped Matthew Fondy in the penalty box, a call that Randolph said was correct.

“The moral of the story is the better team lost,” Wynalda said. “I’ve been watching Chicago for a while, hat’s off to them, they won the game. But it’s pretty clear the referee had his inclusion in this one. I’ll probably get fined for that.

“I’m devastated for my team because they don’t deserve that.”

Wynalda’s anger wasn’t directed at the ref in Wednesday’s game, even after the penalty kick and the red cards given to Chicago’s Mike Magee and the Silverbacks’ Jesus Gonzalez in the 31st minute.

His anger goes back to the Silverbacks’ last game, a 2-1 win over Colorado. In that victory, Wynalda, assistant Ricardo Montoya and key players Jaime Chavez, Kwadwo Poku and Borfor Carr were given red cards. Neither the players not the coaches could participate in Wednesday’s game as a result. Wynalda and Montoya watched most of the game from the media area.

“There’s an undercurrent here that I probably shouldn’t discuss,” Wynalda said. “Players win games and coaches lose games sometimes, but referees ruin them. It keeps happening to us.”

Though Wynalda was obviously unhappy with that referee, he may need to save some of his anger for his team’s finishing on Wednesday.

The Silverbacks outshot Chicago 15-7, but the Fire put more on goal, 6-5, though most of those came in the game’s final 10 minutes. Chicago entered the game with two wins, four losses and a league-high 10 ties in MLS, giving the Silverbacks confidence that they could knock off their third consecutive MLS team in the tournament.

“To outplay them the way we did and to walk away losers is a hard thing to swallow,” Wynalda said.

The Silverbacks wasted a scoring opportunity in the fifth minute when Chicago’s Sean Johnson, a Lilburn native, came out of his goal to stop Junior Sandoval’s shot in a one-on-one situation. Sandoval ran onto a long pass from Blair Gavin, but couldn’t do anything from the tight angle.

Sandoval tried again in the seventh minute, pushing a left-footed shot just wide of Johnson’s far post as Atlanta continued to dominate possession.

Chicago wasted the next chance, with Quincy Amarikwa taking one too many touches in the penalty box in the 11th minute, giving the Silverbacks defense enough time to arrive and clear the danger.

The Silverbacks kept up the pressure with Junior Burgos putting a right-footed shot from 18 yards into Johnson’s arms in the 17th minute.

Burgos tested Johnson again, this time with a curling right-footed shot to the far corner that was pushed over the bar for a corner kick in the 20th minute.

Chicago took a 1-0 lead against the run of the play in the 50th minute when Amarikwa tapped in from point-blank range after another player’s shot deflected off goalkeeper Derby Carrillo.

Atlanta tied the game in the 54th minute when Sandoval beat Chicago’s defense to a long pass down the middle. Instead of taking a shot in the one-on-one with Johnson, Sandoval laid it across to Deon McCaulay for the easy put away.

“Our reaction was very good,” McCaulay said. “We had a lot of opportunities in the first half that we couldn’t convert, but it was a good feeling to come back and tie the game 1-1.”

Chicago grabbed its next lead when Randolph tripped Fondy. Larentowicz blasted his shot down the middle as Carrillo dove to his left.

“I got a little bit of him,” Randolph said. “Foul … not a foul? I’m always going to say no, but it was a PK.”

Atlanta missed a chance to tie in the 84th minute when Alex Harlley’s left-footed shot sailed over the crossbar.

Chicago increased its lead to 3-1 on a counter-attack scored by Alex in the 85th minute.

“This is really hard to take,” Wynalda said.