Tensions flared further in the second half with the teams locked at 1-1 when San Jose coach Matias Almeyda was sent from the sidelines by referee Chris Penso.
Major League Soccer record goalscorer Chris Wondolowski soon followed his coach from the bench. The striker, who was substituted in the 61st minute, was given the first red card of his career for foul and abusive language in injury time.
“In the second half, we fought like lions, which is something that makes me really proud,” said Quakes defender Florian Jungwirth after the game. ”To lose in a way like the way we did tonight would make me cry. It really hurt.”
Following the heated encounter, Almeyda laid the blame with the referee, claiming it was "not a fair match" and describing the Quakes a "clean team."
As they look to secure a place in the Audi 2019 MLS Cup Playoffs, San Jose will be without Espinoza, Wondolowski and Almeyda for Wednesday’s clash at home to Eastern Conference high-flyers Philadelphia Union.
Almeyda was also ejected from the sidelines against LAFC during Heineken Rivalry Week on Aug. 21. During his three-game absence, San Jose went 2-1-0 under the guidance of former Chivas and Cruz Azul coach Benjamin Galindo.
San Jose have fared less well in 2019 without the attacking threat of Espinoza. In three games in which the Argentine failed to suit up, San Jose were winless, losing at New England Revolution and Colorado Rapids and tying D.C. United.
The Quakes' 3-1 loss to Atlanta, courtesy of goals from Justin Meram, Emerson Hyndman and Pity Martinez, leaves them in sixth place in the Western Conference standings with a record of 13-13-5 going into their final three games of the regular season.