According to Russian media, Yakin will receive a salary of 1.6 million euros a season at the side who finished sixth in the 2013-14 Russian Premier League.
"I'm very happy to take charge of a club with such great tradition. Even during our negotiations in Moscow, it was clear to me how serious and professional Spartak were," Yakin said in a news conference on Monday.
"For me it's a great challenge and I hope my coaching staff will cope with the task of securing at least a top three finish."
The former Grasshoppers, FC Basel and Swiss international midfielder retired as a player in 2006. After hanging up his boots, he had coaching stints at Concordia Basel, Thun and Luzern before taking over at Basel in October 2012.
He opted to leave the club on May 17 after Basel had secured their fifth successive domestic title and had been linked with the vacant managerial post at Premier League side Southampton.
Yakin's appointment means Spartak have changed their coach three times in as many months after Valery Karpin was dismissed in March following a poor run of results with Dmitry Gunko taking his place in a caretaker role.
Spartak had started the season well and even led the standings for a few weeks early in the campaign before slipping down to a sixth-place finish that earns them a spot in the second qualifying round of the Europa League.
(Editing by John O'Brien)
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