In means the Hammers are still waiting for their first pre-season win after a 2-2 draw with Czech side Slovacko 24 hours earlier.
Slaven Bilic had sent out a strong side against a side which finished 10th in the Russian league last season.
The starting line-up included captain Mark Noble, Aaron Cresswell, Michail Antonio, Gokhan Tore and impressive new signing Sofiane Feghouli.
Rubin took the lead after 23 minutes when Ilzat Akhmetov escaped Noble's challenge and crossed for Marko Devic to turn in.
West Ham manager Slaven Bilic and assistant manager Nikola Jurcevic
Hammers yet to win this pre-season
A poor pass across the face of his own 18 yard box from Declan Rice allowed Maxime Lestienne to make it 2-0 before Rubin wrapped up the win when Gokdeniz Karadeniz burst through the defence and fired past Adrian.
The Hammers registered just two shots on target in the 90 minutes.
West Ham co owner David Sullivan
No sign of new strikers
And their woes up front don't look like being eased by new signings anytime soon with co-owner David Sullivan admitting on the club's official website this week they are struggling to convince top class strikers to join.
It has left Hammers fans, 52,000 of whom have signed up for season tickets at the club's new 60,000 seater Olympic Stadium, feeling somewhat frustrated.
West Ham's Dimitri Payet
'Nothing without payet' - Twitter reacts
Here's how Twitter reacted to West Ham's 3-0 defeat to Rubin Kazan defeat.
@whufc_official you're relegation contenders without Payet, his back must ache from all the carrying he has to do.— Matthew (@EFCMatthew) July 20, 2016
@whufc_official Funny how so many fans from other clubs need to comment. Obsessed— Sam ⚒ (@samtompkins) July 20, 2016
@whufc_official every time we have a bad pre-season, we have a good season. It always happens lads, we didn't play our best team and if we— Dan (@LittleLanzini) July 20, 2016
@whufc_official considering we were unbeaten in preseason under Avram Grant...— Joe Sullivan (@Joe_Sulli) July 20, 2016
@whufc_official did then we probably would have smashed them 8-0 or even more so just relax guys the owners will sign a great striker— Dan (@LittleLanzini) July 20, 2016
@whufc_official why would we play 2 games in as many games, just asking for injuries.— Tommy (@tommyhaggerty1) July 20, 2016