Owen Coyle's Championship side was unable to prolong its unbeaten start in continental competition as it was undone by Oleg Kuzmin's goal midway through the first half
Oleg Kuzmin's strike after 22 minutes settled the match in the hosts' favor as they moved five points clear at the top of Group D.
Wigan traveled to Russia having secured a 1-1 draw in the last meeting between the two sides at the DW Stadium earlier in the month.
The Championship club knew it could take a big step towards qualification to the next stage with a win, but its hopes were dented as it produced a disappointing performance.
Rubin was in control for the majority of the game and deserved the three points as it seeks to improve on last year's showing in the competition, when it reached the quarterfinals.
Wigan boss Owen Coyle opted to shuffle his pack as he made six alterations to the side that beat Huddersfield Town 2-1, Roger Espinoza making his first European appearance to form part of a five-man midfield.
The visitors' plan to stifle the Russian outfit appeared to be working in the early stages, with both sides struggling to create opportunities.
However, Coyle's men found themselves behind midway through the opening half, as Kuzmin lashed home at the far post after being played through by Bibras Natcho.
Wigan finally crafted its first chance of the encounter as striker Grant Holt headed Espinoza's left-wing cross over the bar.
Rubin dominated for long periods, but it took until the 63rd minute for the Russian side to carve open another genuine goalscoring opportunity, midfielder Alexander Ryazantsev shooting wide from the edge of the area.
Kuzmin headed off target from a corner as Berdyev's charges looked to press home their superiority, but it was Wigan which looked the more likely to score in the closing stages.
And Wigan should have leveled seven minutes from time when Norwegian defender Thomas Rogne headed against the bar, but Coyle's men were left to rue what might have been.