Until substitute Vitolo's 88th-minute contribution, the Czech side were heading to pole position themselves thanks to Michael Rabusic's first-half opener.
They protected it well and rarely looked like conceding after it, but when goalkeeper Premysl Kovar was sent off it changed the game and gave Sevilla a route back in.
They made sure they took it too and they now have a five-point cushion on third-placed Freiburg, meaning they could secure progression in the next round of fixtures.
Starting the night with a 100 per cent record, Sevilla began in a manner befitting of a side in control of the group with Andujar Coke whipping an effort just wide, but Liberec slowly settled and started to make chances of their own.
Sergiy Rybalka's free-kick was mopped up by Javi Varas and then, with 20 minutes gone, they took the lead.
David Pavelka made it, passing from the left on the counter, with Rabusic on the spot to finish from close to the penalty spot.
Sevilla responded with Coke's volley which was dealt with by Kovar, but Liberec remained the more dangerous and Rybalka was unfortunate to see a shot saved by Varas.
Whatever was said by Unai Emery at half-time had little immediate impact on his players as Liberec continued to impress after the restart.
Rabusic hit just over and then Varas had to use his fingertips to deny Josef Sural, before the Spaniards stirred and Juan Cala headed over.
Carlos Bacca then dragged a strike just away from goal and Diego Perotti also chipped in with a shot, but goalkeeper Kovar was barely having to work for his wage.
Perhaps his lack of action cost him in the focus stakes as he was soon hauling down Bacca and receiving his orders (78), but off-target efforts from Perotti and Cala barely upped the ante.
An equaliser would arrive, though, with Vitolo on the spot to tuck away Kevin Gameiro's late cross.