The Russian side were on course for victory after Ari da Silva Ferreira gave them the lead two minutes before the break but Eto’o turned home a Leighton Baines cross to ensure Roberto Martinez’s men remain unbeaten in the group.
Krasnodar made the better start and Mauricio Pereyra shot over the bar from long range in the very first minute before Marat Izmailov’s flick was just too high.
Tim Howard then pulled off a good stop to keep out a low Izmailov shot and the Everton keeper also tipped an Artur Jedrzejczyk effort around the post.
But Everton then settled into the game and began to pose a threat themselves, Andriy Dikan being called into action to keep out a powerful Aiden McGeady effort and a Gareth Barry curler.
John Stones then came within inches of giving the visitors the lead but his looping header was just too high.
However, Krasnodar took the lead just two minutes before half-time when Odil Ahmedov’s speculative through-ball was allowed to reach Ari via an inadvertent Phil Jagielka flick-on and the Brazilian forward produced a delightful volleyed finish.
The hosts pressed for a second goal after the break and Ahmedov should have done better than smash his shot at Jagielka after Tony Hibbert had blocked an Izmailov effort.
An Ari shot landed on the roof of the net after hitting Baines and substitute Wanderson went even closer just minutes after coming on, hitting the crossbar after weaving his way past several defenders and into the heart of the Everton box.
But Everton held out and then managed to find an equaliser with less than 10 minutes to play.
Krasnodar attempted to counter from an Everton corner but ran into trouble and Eto’o swept the ball out to Baines on the right before racing into the box and managing to divert the full-back’s cross past Dikan from close range.
And, having been second best for much of the tie, Everton almost snatched a late winner, only for Dikan to produce a good stop to keep out a downward header from Romelu Lukaku, who had come on at half-time and got up well to meet another Baines cross.