Since the Portuguese coach replaced Luciano Spalletti in mid-March he has overseen three straight victories and Zenit - last season's runners-up - now lead the way with seven games remaining. Substitute Jose Salomon Rondon scored a remarkable hat-trick from the bench while Danny notched and Hulk plundered two penalties.
Shell-shocked Rubin, who slipped into tenth place, responded with goals from Sardar Azmoun and Roman Eremenko. Deposed leaders Lokomotiv Moscow are now two points behind Zenit and host struggling Volga on Monday night.
While Zenit's star is in the ascendant, Dinamo Moscow were taught a harsh lesson by Anzhi Makhachkala. Dan Petrescu's men have challenged for the title all season long but dropped to fourth courtesy of a 4-0 humbling by basement boys Anzhi. Alexander Bukharov, Fedor Smolov, Serder Serderov and Makhach Gadzhiev scored the goals for the Dagestan outfit, who remain five points adrift of safety.
Elsewhere, Rostov climbed to seventh by clinching a 2-0 victory at Krasnodar. Zhano Ananidze opened the scoring shortly before the break and Artem Dzjuba's late penalty rubber-stamped the result.