The Toffees were on the back foot for much of the opening hour of the Group H contest, with Krasnodar taking the lead shortly before the break through a composed finish from Ari.
However, Eto'o met a cross from Leighton Baines with eight minutes remaining to earn the Premier League side a valuable point in Russia.
Napoli put their inconsistent domestic form behind them to see off Slovan Bratislava 2-0 in Group I, with goals by Marek Hamsik and Gonzalo Higuain in each half sealing all three points for the Partenopei.
Group G saw Feyenoord record a 2-1 win against Standard Liege, with Elvis Manu scoring in the 84th minute for the Dutch giants, while Sevilla seized a 2-2 draw away at Rijeka after Stephane M'Bia struck in injury time.
Fiorentina recorded arguably the result of the day so far with a 3-0 thrashing of Dinamo Minsk in Group K, Alberto Aquilani striking in the first half and Josip Ilicic and Federico Bernardeschi scoring in the second period, while a Sylvain Marveaux brace was enough for Guingamp to beat PAOK Salonica by a scoreline of 2-0.
Results in full: Dynamo Moscow 1-0 PSV, Feyenoord 2-1 Standard Liege, Rijeka 2-2 Sevilla, FC Krasnodar 1-1 Everton, Wolfsburg 1-1 Lille, Slovan Bratislava 0-2 Napoli, Sparta Prague 3-1 Young Boys, Aalborg BK 1-0 Rio Ave, Dynamo Kiev 3-1 Steaua Bucuresti, Dinamo Minsk 0-3 Fiorentina, Guingamp 2-0 Salonika, Lokeren 1-0 Metalist Kharkiv, Trabzonspor 0-1 Legia Warsaw