Full back Sergei Ignashevich and forward Arten Dzyuba set up the 2018 World Cup hosts' third win in as many matches since Leonid Slutsky took over in August from sacked Italian Fabio Capello.
Eugeniu Cebotaru was on target for Moldova
"Today I set my men to play the combinational style football from the start," Slutsky said.
"We dominated play in the first half but failed to find the net as Moldova defended well and because of the poor quality of the pitch here.
"After the break we relied on long balls and it worked well as we've scored twice in dead ball situations.
"The home team's late goal was an unpleasant surprise for us as it sent the match into a nervous ending.
"Luckily, we survived Moldova's late storm. I think we've won deservedly tonight."
The win tightened Russia's grip on the runner-up spot in Group G, and a point will now suffice in their closing qualifier against Montenegro next week to secure an automatic ticket to France.
Sweden, their rivals for the coveted second place berth behind runaway table toppers Austria, are third, two points adrift.
Moldova, spurred on by a capacity 12,000 home crowd at the Zimbru arena, tried to take the visitors' goal by storm in an attempt to record their first win of the campaign but Russia soon regained the initiative.
Russia's only serious chance in the first half came in the 28th minute when forward Alexander Kokorin went close with a header after a pinpoint cross from right-back Oleg Kuzmin.
In the 55th minute Kokorin forced Moldova goalkeeper Alexei Koselev into a diving save to deny his 22-yard low shot.
Three minutes later striker Artem Dzyuba stopped a freekick by Dmitry Kombarov with his chest in the area to feed Ignashevich, who hammered the ball past helpless Koselev from close range.
In the 78th minute Dzyuba doubled Russia's advantage, sending the ball into the net after a well-served corner by Kombarov.
Midfielder Cebotaru pulled one back for Moldova with five minutes to go, when he headed the ball home from the edge of the six-yard box also after a corner.