SAN JOSE >> The Earthquakes failed to protect a pair of one-goal leads and team captain Cristian Espinoza exited early with a gashed leg en route to their ouster from the U.S. Open Cup on Tuesday night.

Austin FC prevailed in penalty kicks to beat San Jose in a heated quarterfinal before 10,754 at a half-filled PayPal Park.

The Earthquakes gave up a 1-0 lead in regulation and a 2-1 cushion in the first of two 15-minute overtimes before falling 4-2 in penalty kicks. Both of Austin’s tying goals came on penalty kicks before the shootout ultimately decided the three-hour affair in which tempers flared and yellow cards flew.

The Earthquakes had to finish without Espinoza, a second-half substitute who hobbled off with a severe cut above his right knee when struck by a high kick from Mikkel Desler, about four minutes into extra time.

“That foul on him is a straight red card. The officiating was comical,” San Jose coach Bruce Arena said.

Instead, Desler drew a yellow card -- Austin’s fourth on the night -- from referee Brandon Stevis, who then was confronted and berated by Espinoza once he got off the ground near midfield.

Officials declined to respond to postgame questions from a pool reporter.

Espinoza’s wound required 10 stitches, according to a team spokesman. Arena said he’s unsure of Espinoza’s availability for Saturday’s game at Minnesota. When Espinoza reached the Earthquakes’ bench, he showed his open wound to the sideline camera and retreated to the locker room for treatment.

“There were a lot of emotions going on seeing your captain go down with a gash on your leg,” San Jose defender Jamar Ricketts said. “The ref was saying there wasn’t enough contact or it was ‘too soft.’ That’s what had everyone riled up. If it was too soft, there wouldn’t be a 2-inch gash on our captain’s leg.”

Espinoza was not made available for comment after the game. He was dressed in jeans as he was driven in a golf cart to his car in the parking lot where awaiting fans chanted his name in support.

In the shootout, San Jose’s Chicho Arango and DeJuan Jones had their shots blocked, and Austin made its first three attempts – by Diego Rubio, Myrto Uzuni and Robert Taylor – before Owen Wolff’s clincher.

Arena took umbrage not only with the on-field officiating but the video assistant referee system, saying: “The VAR was useless today. There were a bunch of plays and they ignored everything.”

Austin’s semifinal appearance won’t come for nearly two months, on either Sept. 16 or 17, at Minnesota United FC, which advanced with a 3-1 win Tuesday night against Chicago. If Minnesota wins, it will host the U.S. Open Cup final Oct. 1 at Allianz Field.

Benji Kikanovic put the Earthquakes in position to win in extra time with a 99th-minute, go-ahead goal. It capped a bewildering 13-second, four-shot sequence in the penalty box, starting with Martinez’s 12-yard shot off the crossbar. Then came an Ian Harkes shot that appeared to ricochet off a defender’s hand. Another Martinez shot got blocked before Kikanovic collected the ball and blasted in his first goal of the season.

Kikanovic, a San Jose native and Sacramento State product, delivered his right-footed scoring strike in the first of two 15-minute extra time periods, and the Earthquakes failed to protect their late lead.

Austin countered with its second goal off a penalty kick, this overtime one provided by Uzuni, whose shot into the lower right of the net mirrored the 65th-minute penalty kick by teammate Brandon Vazquez that tied the score at 1. Quakes midfielder Mark-Anthony Kaye tripped up Wolff at the edge of the 18-yard box off a corner kick to draw the penalty.

The Earthquakes went ahead 1-0 when Arango one-timed Ousseni Bouda’s centering cross near the top of the penalty box.

Vazquez pulled Austin even at 1 by converting a 65th-minute penalty kick, following a foul in the box by Earthquakes defender Max Floriani. Prior to Vazquez’s shot into the lower-right side of the net, goalkeeper Daniel drew a yellow card for dissent as he argued the foul call.

Vazquez left in the 71st minute on a stretcher with an apparent ankle injury.

Locked in a 1-1 draw, Arena summoned two of his stalwarts off the bench in the 76th minute: Espinoza (second in MLS assists) and Martinez (second on the team in goals). Kaye was also out of the starting lineup but came on to replace Beau Leroux in the 59th minute and remains the only Earthquakes player to appear in every game this season.

In the 81st minute, Espinoza unsuccessfully pleaded for a penalty kick after getting tangled near the end line with Austin defender Zan Kolmanic. A minute later, Arango had two shots blocked toward a seemingly open goal. Daniel kept it 1-1 with a close-range save just as officials announced eight minutes of extra time in regulation.

Unbeaten in 12 of their previous 13 games, the Earthquakes’ last loss before Tuesday came May 31 at St. Louis.

The Quakes’ next game is Saturday in Minnesota as they return to MLS regular-season play, where they are sixth in the West with 28 points. Austin (26 points, 10th in West) will return to PayPal Park for the regular-season finale Oct. 18.