A brace by Oleg Shatov and goals from Alexander Erokhin, Artem Dzyuba, and Sebastian Driussi steered the Saint Petersburg’s side to a well-deserved win, leaving them seven points clear of second-placed Rostov.
Spartak Moscow sit third with a worse goal difference.
“It was a good game,” Zenit head coach Sergei Semak said. “We netted five and could have scored even more. We looked better, we performed quality football, and won deservedly today.”
“Though we’ve conceded three goals, I’d say that we played not bad in defence. It’s a pity that we failed to avoid a nervous ending, but all’s well that ends well.”
Zenit, the league’s only unbeaten side this season, started in a lively fashion, pinning Lokomotiv back, and in the 13th minute Shatov put the hosts 1-0 up.
The visitors replied positively and their midfielder Dmitry Barinov pulled them level just four minutes later, hammering the ball home from 23 metres out.
Russian international forward Erokhin restored Zenit’s lead three minutes after the interval before Dzyuba scored Zenit’s third, while Shatov netted his second of the match after the hour mark.
But Lokomotiv refused to surrender and Aleksei Miranchuk reduced the arrears with a close-range shot in the 74th minute.
Lokomotiv’s hopes of turning the match around suffered a serious blow in the 82nd minute when their midfielder Dmitry Tarasov, who was substituted into the game just four minutes earlier, was sent off for a second bookable offence.
Nevertheless, Russian international forward Fyodor Smolov scored the Moscow team’s third goal in the 86th minute.
But Driussi dashed Lokomotiv’s chances mercilessly with less than a minute to go, when he rounded off the scoring.
In the other Sunday encounter, Spartak and CSKA played out a 1-1 draw in Moscow’s ferocious derby.
CSKA dominated the play, but it was Spartak’s Brazilian midfielder Fernando who opened the score with a well-struck free kick just before the half-hour mark.
After the break the hosts upped the tempo, and in the 63rd minute their Croatian midfielder Nikola Vlašić levelled with a shot from the edge of the area.
CSKA, fresh from their success and spurred by a 30,000-strong home crowd, poured forward in attack seeking the winning goal but failed to find the net lacking a killer instinct in front of Spartak’s net.