What ultimately proved to be the decisive moment of the Group D match - which has the Kazan Kremlin as a dramatic backdrop - came in the 22nd minute when Oleg Kuzmin latched on to a lofted ball into the area and cracked it home.
The effort seemed to go right through 21-year-old goalkeeper Lee Nicholls, who was making his European debut in only his fifth senior Latics appearance.
But given the ferocity of Kuzmin's shot, the England youth international appeared to have little chance of keeping it out.
It was the only real display of potent attacking from either side in a subdued first half, but Wigan stepped things up after the break and came close to equalising.
Thomas Rogne sent a header against the bar and late on James McClean's touch diverted the ball just the wrong side of the post.
The leveller would not come, though, as group leaders Rubin - who Wigan drew 1-1 with at the DW Stadium in their last European outing - claimed all three points.
The Russian outfit now have 10 points, while Wigan have five, with both teams having played four games.
Around 150 Latics supporters had made the lengthy journey from Wigan and they saw their team take a while to get going.
Rubin settled quicker and won a corner in the 12th minute that led to Aleksandr Ryazantsev miskicking when well placed in front of goal.
Two corners in quick succession then followed for Wigan, with the second creating a brief moment of panic for Rubin in their box before they managed to clear.
Moments later, Rubin were in front as full-back Kuzmin ran on to Bebras Natcho's ball forward and drilled his shot beneath Nicholls.
Ryan Shotton misplaced a pass at the back soon after and Ryazantsev looked to take advantage, firing wide from outside the box.
Wigan tried to generate some momentum and Grant Holt headed over from Roger Espinoza's cross.
The Latics then made a couple of blocks to repel Rubin and Espinoza burst forward on the counter-attack before taking a tumble in the box under the attention of the home defence, with no penalty being awarded.
McClean sent a free-kick into the area but it bounced out with no-one having been able to apply a finish and Sergei Ryzhikov then had little trouble catching a header from Holt.
Ryzhikov looked a little more flustered when trying to punch away Stephen Crainey's free-kick just before half-time, but his defence cleared up.
The goalkeeper was in trouble again early in the second half when Shotton's long throw into the box deceived him and Leon Barnett sent the ball against the bar, but the flag was up from the referee's assistant.
Nicholls then did well, coming out and getting down at the feet of Ruslan Mukhametshin, before Ryazantsev shot wide as Rubin began to look dangerous again.
Nick Powell, who had come on for James Perch, found some space nicely before lashing an effort wide from distance, but Rubin were soon back on the attack as Rogne got himself in the way of Ryazantsev's shot.
Coyle shuffled his pack further, bringing on Marc-Antoine Fortune and Jordi Gomez for Holt and Callum McManaman.
And Fortune sent a shot into the side netting, before Rogne went even closer to bringing things level, with his looping header hitting the bar.
McClean also nearly made it 1-1 in the closing stages as the ball came off him from Gomez's corner and flashed wide.
At the other end, Nicholls made a good save while the flag was up for offisde and then spilled the ball, which came to Ryazantsev, who scooped off-target.