Vicente Iborra opened the scoring in the first half and substitute Raul Rusescu's late goal clinched victory for Sevilla.
The result left the hosts vulnerable to Liberec, who duly beat Estoril 2-1 in Portugal to snatch second place in Group H.
Freiburg threatened inside two minutes when Pavel Krmas' header was parried at close range by keeper Javi Varas, and Sevilla responded with a shot over the bar by Ivan Rakitic.
It was an otherwise quiet opening, enlivened only when Juan Cala was booked for fouling Freiburg's Vladimir Darida and Admir Mehmedi curled the resulting free-kick goalwards. Varas was again equal to it.
Diego Perotti drew a save from Oliver Baumann with a 30-yard effort and then turned provider as Sevilla took the lead five minutes before half-time.
The Argentinian winger produced some trickery on the left and cut the ball back into the six-yard box, where it was bundled home by the towering Iborra.
Freiburg were unable to equalise before the interval, Matthias Ginter heading over from six yards.
Varas dealt with Ginter's long-range effort but almost gifted Freiburg an equaliser when he promptly cleared the ball against Gelson Fernandes, who lashed wastefully over when Mehmedi nodded it back into his path.
Nicolas Hofler was booked for knocking the ball in with his hand after Varas saved his initial header, though the midfielder seemingly had time to control the ball and score a legitimate goal.
Varas held Sebastian Kerk's long-range shot but Sevilla took the upper hand, Perotti's 20-yard effort saved before Jairo hit the post.
The Spanish side should have put the game to bed in the 80th minute when three players broke clear, pursued by defenders but with only Baumann to beat Rakitic squared the ball to Perotti, but his weak shot was brilliantly saved.
Rakitic shot over after another break but Rusescu made no mistake in the fourth of seven additional minutes, timing his run perfectly to avoid an offside flag as he latched on to Jairo's flick and finished low past Baumann.