Match ends, Rubin Kazan 1, Wigan Athletic 0.
Wigan Athletic produced a brave display but left Russia empty handed as Oleg Kuzmin's strike put Rubin Kazan into the Europa League knockout stages.
Kuzmin fired home a low effort in the first-half after a long ball over the top caught the Wigan defence out.
Grant Holt then headed over for Owen Coyle's side before substitute Nick Powell shot just wide after the break.
Wigan continued to push for an equaliser but Thomas Rogne's late header came back off the bar.
Despite their first Europa League defeat, Wigan's hopes of progressing to the knockout stages remain in their own hands with a home tie against Belgium side Zulte Waregem and a visit to Slovenia to face Maribor to come.
This was always going to be a tough ask for the Championship outfit against a side who have not lost in Kazan in 22 European games. But they will feel frustrated as one lapse of concentration cost them a valuable point.
After a scrappy start, Aleksandr Ryazantsev should have put Kazan in front, but he completely mishit the ball from just eight yards out.
Wigan did not heed the warning, though, and when winger James McClean switched off it allowed Kuzmin the space to break in behind the defence and score the opener.
The visitors, who held Kazan to a 1-1 draw at the DW Stadium a fortnight ago, started to edge their way into the game and their Russian hosts seemed hesitant when the Championship side delivered high balls into the area.
That tactic should have brought Wigan an equaliser after the half hour mark when Roger Espinoza delivered a superb cross-field pass that found Holt free, but the former Norwich striker headed well over from 12 yards despite having time and space to control ball.
Kurban Berdyev's side seemed content with their slender advantage and only threatened the visitors with the odd counter attack.
Powell, who scored the equaliser in the reverse fixture, came on after the break and the on-loan Manchester United forward went close with a long-range effort with 22 minutes to go after losing two Kazan defenders with ease.
Espinoza then delivered a superb cross that Rogne rose well to meet, but his header came off the bar before McClean's late flick from Stephen Crainey's corner went agonisingly close.
Wigan manager Owen Coyle:
"I think at the outset, everybody felt - and rightly so - that Rubin would be the favourites to win the group.
"But with what we have shown in the two games, home and away against Rubin, we are confident going into our last two group games.
"We have the quality to progress from the group.
"We have to keep putting in performances like tonight and if we do that it will see us earn enough points to qualify for the knockout stages.
"On another day it would have resulted in not even a draw but a win for us.
"There are a lot of positives and is a lot to be pleased about."
- 22MavingaSubstituted forKislyakat 45'minutes
- 44NavasBooked at 55mins
- 81MukhametshinSubstituted forPrudnikovat 84'minutes
- 10TorbinskiBooked at 40minsSubstituted forMubarakat 76'minutes
- 23Alekseevich Eremenko
- 3CraineyBooked at 66mins
- 24PerchBooked at 35minsSubstituted forPowellat 60'minutes
- 9HoltSubstituted forFortunéat 71'minutes
- 15McManamanSubstituted forGómez García-Pencheat 74'minutes
- 11McCleanBooked at 70mins
- 14Gómez García-Penche
- Hüseyin Göçek
- Shots on Target
Second Half ends, Rubin Kazan 1, Wigan Athletic 0.
Aleksandr Ryazantsev (Rubin Kazan) wins a free kick in the defensive half.
Foul by Roger Espinoza (Wigan Athletic).
Attempt blocked. Jordi Gómez (Wigan Athletic) left footed shot from outside the box is blocked.
Foul by César Navas (Rubin Kazan).
James McArthur (Wigan Athletic) wins a free kick in the attacking half.
Attempt missed. Wakaso (Rubin Kazan) left footed shot from outside the box is high and wide to the left. Assisted by Aleksandr Ryazantsev.
Attempt missed. Aleksandr Ryazantsev (Rubin Kazan) right footed shot from the left side of the box is high and wide to the right. Assisted by Aleksandr Prudnikov.
Attempt saved. Wakaso (Rubin Kazan) left footed shot from long range on the left is saved in the centre of the goal. Assisted by Sergei Kislyak.
Attempt missed. James McClean (Wigan Athletic) left footed shot from the centre of the box misses to the left. Assisted by Jordi Gómez with a cross following a corner.
Corner, Wigan Athletic. Conceded by Yann M'Vila.
Offside, Rubin Kazan. Roman Eremenko tries a through ball, but Aleksandr Prudnikov is caught offside.
Attempt missed. Jordi Gómez (Wigan Athletic) left footed shot from outside the box is close, but misses to the left following a set piece situation.
Substitution, Rubin Kazan. Aleksandr Prudnikov replaces Ruslan Mukhametshin.
Foul by Wakaso (Rubin Kazan).
James McArthur (Wigan Athletic) wins a free kick in the defensive half.
Attempt blocked. Thomas Rogne (Wigan Athletic) left footed shot from outside the box is blocked. Assisted by Nick Powell.
Thomas Rogne (Wigan Athletic) hits the bar with a header from the centre of the box. Assisted by Roger Espinoza with a cross.
Offside, Rubin Kazan. Bebras Natcho tries a through ball, but Aleksandr Ryazantsev is caught offside.