A Fernando Torres double and a powerful finish from Victor Moses gave the Blues a strong lead heading into the return leg - which will be held at Luzhniki Stadium, the scene of their 2008 Champions League final defeat, after Rubin's Tsentrainiy Stadium was deemed unsuitable for use by Uefa.
Bibras Natkho's first-half penalty handed the Russian outfit a valuable away goal, and Benayoun is aware that his team face a tricky tie on April 11.
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"We started very well and after scoring we felt we could score three or four and finish the game, but it changed with the penalty, it gave them confidence and allowed them back in the game.
"It was important to score the third goal, it's a good result but we still need to complete the job next week and it will be very hard in Moscow."
Benayoun played 83 minutes against Rubin Kazan - his first start for Chelsea since March 7 - and says he felt sharp and confident after nearly a month of second-half cameos in the Premier League.
"It's not easy, there are a lot of good players here but I felt good. I felt sharp from the first minute, I was involved in the game and that gives you confidence," Benayoun continued.
"When the team plays well it's easier, you get involved and try more things, so it was good for me. When you have confidence you try more, that's normal."