Arturs Zjuzins had an opportunity to fire the home side ahead in the 12th minute as he collected the ball on the edge of the box, but he sent his effort past the post.
Vanins kept the scores level after he made another impressive save, this time to deny Islambek Kuat as he rifled an effort from close range towards the net.
Sergey Khizhnichenko was the next Kazakhstan player to be denied by Vanins as he made a block with his body to close down the angle following a right-footed strike from the midfielder.
The visitors got their breakthrough in the second half when Kuat received the ball in the box and he rifled a left-footed strike beyond the reach of Vanins into the bottom corner.
However, the home side could not find the net to notch a leveller as their closest effort came from Vladislavs Gabovs, who sent his long-range effort over the bar as they succumbed to defeat.