"The club's shareholders made a decision that Unai Emery will no longer coach Spartak," Spartak director general Valery Karpin told reporters, adding that a decision on a new coach will be made in the next few days.
Emery was given a vote of confidence by Spartak owner Leonid Fedun just five days ago following a 3-0 loss to Barcelona in the Champions League, but after a second home beating in a week the axe finally fell on the Spaniard.
Emery was appointed Spartak coach in May, replacing former Russia international Karpin despite the team finishing last season in second place and qualifying for the Champions League.
The 41-year-old was given a two-year contract after he led Valencia to three consecutive third places in Spain behind Barcelona and Real Madrid.
Spartak, Russia's most successful and popular club with nine league titles between 1992 and 2001, have not claimed any domestic trophies since winning the Russian Cup in 2003.
They started this season well but then fell into a slump after a spate of injuries to several leading players.
They are in seventh place, 10 points behind leaders CSKA Moscow, who travel to St Petersburg to face champions Zenit on Monday.
Spartak have also failed to impress in Europe and have been consigned to finishing bottom of Champions League Group G with a game to spare.
SWEET REVENGE
Sunday's match at the Luzhniki went without major crowd trouble after Dynamo's last match, at home to Zenit last weekend, was abandoned when their goalkeeper was injured from firecrackers thrown by fans.
Dynamo were awarded a 3-0 win after Anton Shunin suffered burns to his cornea in both eyes and some loss of hearing.
This time they earned their points on the pitch as Alexander Kokorin and fellow Russia international Igor Semshov each scored twice to inspire Dynamo, who gained sweet revenge for a 4-0 rout by Spartak in their first meeting this season in August.
That defeat cost Dynamo coach Sergei Silkin his job and he was replaced by ex-Romania and Chelsea defender Dan Petrescu.
Dynamo have steadily moved up the table under Petrescu after a dreadful start. They are ninth, five points adrift of Spartak.
"I think it was Dynamo's best match this season and probably one of the best in my entire coaching career," Petrescu told Russian television NTV.
"It was a good payback for our previous loss to them. If it was a European Cup tie we would have won based on aggregate score," he added with a wry smile.
