The forward struck twice in the second half to leave his side top of the nascent league table on goal difference after a 2-0 win.
Danny scored the only goal as Zenit St Petersburg won 1-0 at Krylya Sovetov, who finished with 10 men after the late dismissal of Ivan Taranov. Anzhi Makhachkala and Spartak Nalchik drew 0-0 in the day's other game.
That took the champions four points clear of second-placed Spartak Moscow with only two matches left of the season.
Alejandro Dominguez scored the opening goal in the 66th minute, and Alexander Bukharov made sure of the points with the second in the last minute.
Third-placed Zenit St Petersburg, out of title contention, beat Terek Grozny by the same score - Fatih Tekke netting both goals.
Spartak Nalchik missed the chance to secure their top-flight status when they were beaten 4-2 at home by Dinamo Moscow.
Alexander Kerzhakov netted twice for Dinamo, who were two up inside 13 minutes.
Amkar Perm also remain in trouble after losing 1-0 against 10-man Lokomotiv Moscow. Charles was sent off in the 56th minute, but Dmitri Sychev scored a last-minute winner.
Spartak closed the gap to one point in the battle for the title as Pavel Yakovlev, Zhano Ananidze and Welliton also got on the scoresheet.
Alexandru Gatcan was the scorer of Rostov's consolation.
Spartak Nalchik beat fellow strugglers Kuban Krasnodar 4-0, with three of the goals coming in the second half.
Shamil Asildarov opened the scoring with a penalty on 32 minutes - and Alexander Amisulashvili (64), Vladimir Kisenkov (76) and Leandro (90) completed the rout.
Lokomotiv Moscow remain in the hunt for a European place following a 3-1 away win against Tomsk, where both sides had a man sent off with half-an-hour remaining.
Dmitri Sychev (11) opened the scoring, and Goran Maznov equalised for Tomsk nine minutes later.
Sychev restored the visitors' lead, and Peter Odemwingie completed the scoring - before Artem Dzjuba and Ruslan Kambolov were both dismissed.
Following a scoreless first half, the defending champions came to life with goals from Cristian Noboa and Alexander Bukhavor before the hour mark.
Veteran striker Jan Koller got one back for the visitors soon afterwards. But they were given no chance to find an equaliser as Gokdeniz Karadeniz restored the two-goal advantage almost immediately - and then Bukharov's second sealed the win.
The win puts Rubin four points clear of Spartak Moscow, who play Rostov tomorrow.
CSKA Moscow have moved up to fourth, for 24 hours at least, after edging out Terek Grozny 1-0 courtesy of Tomas Necid's third-minute strike.
Neighbours Saturn Moscow were also 1-0 winners tonight, beating FC Khimki through a 49th-minute goal from Denis Halilovic.
Rubin, who stunned Barcelona at the Nou Camp in the Champions League in midweek, led 2-0 at half-time thanks to goals from Alejandro Dominguez and Cristian Ansaldi.
Mersudin Ahmetovic pulled one back at the start of the second period but the visitors held on to re-establish their one-point advantage over Spartak Moscow.
Zenit St Petersburg lost ground on the top two with a 2-2 home draw against Spartak Nalchik.
Vladimir Bystrov and Fatih Tekke twice put Zenit ahead but David Siradze and Leandro ensured the away side did not go away empty-handed.
FC Moscow moved up to fourth after winning 3-1 at city-rivals CSKA.
The game was effectively over inside 39 minutes as the visitors surged ahead through goals from Dmitri Tarasov, Alexei Rebko and Alexandru Epureanu.
Tomas Necid pulled one back for a below-par CSKA.
Dinamo Moscow drew 1-1 at struggling Kuban Krasnodar while today's other game, between Amkar Perm and Tomsk, finished goalless.
Spartak Moscow moved, temporarily at least, to the top of the Premier Liga as they despatched rock-bottom FC Khimki 3-0.
Welliton put the visitors ahead in the ninth minute before Sergei Parshivlyuk made it two a minute before half-time.
Welliton converted a second in the 88th minute to put the icing on the cake.
Lokomotiv Moscow and Saturn Moscow shared four goals as Lokomotiv twice came from behind to take a point.
Andrei Karyaka opened the scoring with a 32nd-minute penalty before Tomislav Dujmovic levelled. Vladimir Kuzmichev (51) and Dmitri Sychev (88) then traded goals, while Luiz Zelao saw red for Lokomotiv.
Krylya Sovetov beat Terek Grozny 2-0, with Vladislav Ignatiev and Roman Adamov on target.
Goals from Gokdeniz Karadeniz (25) and Alexander Bukharov (49) gave Rubin a cushion before substitute Aleksandr Marenich halved the deficit after 53 minutes.
An Alejandro Dominguez penalty four minutes from time made certain of the points to keep Rubin ahead of Spartak Moscow, who ran out 4-2 winners over lowly Spartak Nalchik.
Two Welliton goals in the first 11 minutes gave Moscow the edge but Nalchik pulled level early in the second half with strikes from Vladimir Kisenkov and Shamil Asildarov.
Vladimir Bystrov restored the visitors' lead after 75 minutes though, and Welliton made sure of the result with a last-minute penalty to complete his hat-trick.
In today's other match, a late double from Denis Halilovic earned Saturn Moscow a 2-0 win at Kuban Krasnodar, who had Alexsey Botviniev sent off after just three minutes.
