Kevin Gameiro's early goal looked to have set Sevilla on their way to victory, but they were hit with a sucker-punch in stoppage time when Estoril, who had threatened only sporadically during the match, snatched an equaliser through Ruben Fernandes.
The match mirrored Sevilla's last European outing, when opponents Slovan Liberec netted a second-half equaliser to claim a 1-1 draw from a game the Spanish side dominated, but fortunately for the 2006 and 2007 Europa League winners it did not prove costly.
Their point from Thursday's match, combined with Freiburg's win at Liberec, means they are now assured of a top-two finish in Group H.
Sevilla, in buoyant mood following their 4-0 derby thrashing of arch rivals Real Betis at the weekend, took the lead after just seven minutes with a clinical breakaway goal.
The influential Jose Antonio Reyes created the chance as he beat two players inside his own half before threading a perfect through-ball for Kevin Gameiro to race on to, and the France international was not about to waste the opening as he lashed a rising shot past Vagner da Silva.
After that it was pretty much all Sevilla in the first half but they could not add to their lead with Vagner parrying Ivan Rakitic's low shot and Coke and Gameiro both failing to hit the target when presented with decent opportunities inside the area.
Estoril's only real opportunity saw Evandro Goebel drill a 25-yard shot straight at home goalkeeper Javi Varas.
Varas was called on again to keep out two efforts Luis Leal after the break as Estoril provided more of an attacking threat, but the hosts kept their noses in front.
Sevilla also had chances to increase their lead, with arguably their best falling to substitute Vitolo six minutes from time when he raced into the area from the left and was only denied by the outstretched left arm of Vagner.
A goal then would have killed the game off, but Portuguese side Estoril made the most of the escape by grabbing an unexpected last-gasp equaliser.
Sevilla lost the ball in their own half and Javier Balboa picked up possession and then fed a pass into the unmarked Fernandes inside the area.
The centre-back took a touch before poking his shot past Varas to stun their Iberian rivals, although it did not prevent Sevilla progressing through to the next round.