The Red Army side moved on to 46 points from 20 matches to stay five points ahead of second-placed Anzhi Makhachkala, which plays at Saransk on Monday (AEDT).
Reigning champion Zenit St Petersburg, which also plays on Monday at Kazan, is third on 38 points.
Though CSKA came to Samara without a slew of first teamers it still started in a lively fashion on the uneven Samara pitch.
The visitor created a set of chances but failed to open the score before the 38th minute when Swedish midfielder Pontus Wernbloom netted his third goal of the season, heading home from Alan Dzagoev's corner.
Nigerian forward Ahmed Musa made it 2-0 in the 72nd minute when he received Vagner Love's pass and dribbled into the box to fire into the net despite a tough challenge from Samara's French defender Steeve Joseph-Reinette.
"It was a tough match under unfavourable weather conditions but we managed to cope with our task and won it," CSKA head coach Leonid Slutsky said.
"We were in control throughout the match and won deservedly. We just were the better side today."
Meanwhile, Dynamo Moscow jumped into the fifth spot with a hard-fought 1-0 win over city rival Lokomotiv.
Dynamo midfielder Ivan Soloviev, just 19, was the hero as he scored in the 20th minute, guiding home a close-range rebound after Lokomotiv 'keeper Guilherme parried Alexander Kokorin's shot from eight metres.
Lokomotiv replied positively and began testing Dynamo's defence but to no avail with keeper Anton Shunin in complete command of his net.
In the 68th minute Dynamo halfback Artur Yusupov was sent off for a second bookable offence. However, Lokomotiv failed to find an equaliser.
"All Dynamo players have worked really hard since I took over the team last year," Dynamo manager Dan Petrescu said. "Now we are reaping the fruits of our hard work.
"It was very important to start with a win after the winter break and luckily we managed to do it. Today we overcame a very strong team with skilled footballers in their line-up."