CSKA Moscow’s 1-1 draw with Rostov on Saturday saw them edge FC Krasnodar for Russia’s second Champions League spot.
FC Krasnodar and Dynamo Moscow now go into the Europa League as third and fourth placed finishers after their 1-1 draw.
CSKA will play in August’s tricky Champions League third qualifying round as they finished second, equal on points with Krasnodar but with more wins this season.
Last year’s champions CSKA Moscow had a tough encounter with Rostov, who needed to win to avoid the relegation play-offs.
CSKA went behind in the last minute of the first half when defender Vitaly Diakov calmly slotted a penalty past ‘keeper Igor Akinefeyev after a foul on Alexander Bukharov in the box.
Sweden midfielder Pontus Wernbloom saved the day for the Red Army side as he levelled at 1-1 with a header.
“I’d like to thank my men for their skills and strong character which they showed today,” CSKA head coach Leonid Slutsky said.
“It was a very hard match as Rostov needed to win. But I think we deservedly finished runners-up this season.”
FC Krasnodar, who missed a chance to leapfrog CSKA as they were held to a 1-1 draw by Dynamo Moscow, felt they’d had a good season anyway.
“It’s a pity that we’ve missed our chance,” FC Krasnodar manager Oleg Kononov said.
“We played better today and had chances to beat Dynamo. But in general it was a very good season for our team.”
Russian champions Zenit St Petersburg ended the Premiership season on a winning note as they beat 10-man Lokomotiv 1-0.
Zenit finished on top of the Premiership table, seven points ahead of CSKA and Krasnodar.
After a goalless opening period at Petrovsky stadium Zenit came out meaning business in the second half, but their striker Salomon Rondon failed to convert a wonderful chance after a pinpoint cross.
Then in the 54th minute Lokomotiv were reduced to 10 men as their midfielder Dmitry Tarasov received a direct red card after a scuffle and Zenit soon made them pay.
The Saint Petersburg outfit’s skipper Miguel Danny helped the ball on to Rondon in the area and the Venezuelan kept his cool, guiding the ball into the far corner from the edge of the six-yard box just past the hour mark.
Torpedo Moscow and Arsenal Tula were relegated.
They will be replaced in the Premiership by Samara and Anzhi Makhachkala.
Third-bottom Rostov and fourth-bottom Ural Yekaterinburg will play in the relegation play-offs with Tosno and Tomsk.