The win was a famous one for Spartak's new manager, Danish soccer legend Michael Laudrup, and will have won him the affection and trust of the club's fans, a necessary requirement for the overhaul of the team that the new trainer reportedly has in store.
Despite unprecedented success in the 1990s, Spartak have not won the Russian title since 2001, and were in sixth place before the start of the match.
CSKA's defeat means that the 2002, 2003, and 2006 champions have now lost all realistic chance of catching runaway leaders Rubin FC, from Russia's republic of Tatarstan. Rubin can seal the championship title tomorrow with a win away to lowly Moscow Region side Saturn FC. Russia's season runs from March to November.
Playing in front of a crowd of 60,000 at the Luzhniki stadium, the ground that both teams call home, CSKA started the better and should have taken the lead on a number of occasions in the first half.
Defender Alexei Berezutsky missed the 2005 UEFA Cup winner's clearest chance, his close-range header going just over the bar in the 27th minute.
CSKA's Brazilian striker Vagner Love also went close just before half-time, Spartak keeper Stipe Pletikosa beating away his vicious shot.
The second forty-five minutes began with Spartak seizing the initiative, and they were rewarded with a goal in the 57th minute, Nikita Bazhenov turning home from close-range after Vladimir Bystrov's pin-point ball into the box.
CSKA, who had won their last 11 games in all competitions, and were unbeaten in 13, hit back. However, Spartak, desperate for the win that would break their seven years of misfortune against CSKA, boost their chances of European soccer next year, and avenge a 5-1 defeat in the corresponding fixture earlier in the season, defended well, and could have caught their opponents on the break on a number of occasions.
Tempers frayed towards the end of the match and CSKA's Russian international Yuri Zhirkov was shown the red card after pushing the referee.
CSKA had a final chance to level the score in the dying seconds, Serbian midfielder Milos Krasic's shot first saved by Pletikosa and then ricocheting off Vagner Love for a goal-kick.
The final whistle followed seconds later, and Spartak's fans celebrated a memorable victory, and one that they hope will herald the revival of the club.
Zenit St. Petersburg play Moscow Region side Khimki later on Saturday in a match they must win to maintain their faltering bid for a 2009/10 Champions League place.
In the 2009/10 season, for the first time, the top three teams in the Russian Premier League will qualify for the Champions League. The top two clubs will go into the group stages, with the third-placed team starting in the second qualifying round. The fourth- and fifth-placed teams will enter the UEFA Cup, while the bottom two sides are relegated.
Table - (After 26 games unless stated)
Rubin - 57
CSKA Moscow - 50 (27 games)
Dynamo Moscow - 44
Spartak Moscow - 43 (27 games)
Zenit St Petersburg - 40
Amkar - 41
Lokomotiv Moscow - 38
Krilya Sovetov -38
FC Moskva -34
Spartak Nalchik - 30
Terek Grozny -30
Tom Tomsk -27