It was a bad night in the Europa League for the Bundesliga clubs as Hertha Berlin, FC Koln and Hoffenheim all suffered defeats in matchday two.
Hoffenheim remain without a point in Group C after they were beaten 2-1 by Ludogorets at the Ludogorets Arena on Thursday.
TSG got off to the perfect start when Pavel Kaderabek opened the scoring just two minutes after the kick-off, but second-half goals from Svetoslav Dyakov (46') and Jody Lukoki (72') secured the comeback win for the Eagles.
Milan lead the way in Group D with a 100% record after they recorded a last-gasp 3-2 victory over Rijeka at the San Siro.
The Rossoneri went into the break with a 1-0 lead courtesy of Andre Silva's 14th-minute opener, before Mateo Musacchio (53') doubled their advantage early in the second half.
But the visitors hit back with two late goals from Boadu Acosty (84') and Josip Elez (90' pen) to seemingly earn a share of the spoils, only for Patrick Cutrone to pop up deep into stoppage time with the winner for Milan.
Atalanta continued their impressive start in Group E after a 1-1 draw with Lyon at the Groupama Stadium kept them in top spot.
Alejandro Gomez (57') quickly cancelled out Bertrand Traore's 45th-minute opener for Les Gones as La Dea remain unbeaten in their group.
FC Koln's woes deepened after they went down 1-0 to Red Star Belgrade at the RheinEnergieStadion, where Richmond Boakye's 30th-minute goal settled matters.
The Billy Goats are still searching for their first win in all competitions this season, as they remain rooted to the foot of the Bundesliga standings and Group H.
Marseille slipped to their first defeat in Group I after Red Bull Salzburg emerged 1-0 victors at the Red Bull Arena, with Munas Dabbur scoring the only goal of the game in the 73rd minute.
Athletic Bilbao suffered a surprise 1-0 reverse against Zorya at San Mames to remain winless in Group J, while Hertha Berlin lost by the same scoreline to Ostersunds at the Jamtkraft Arena.
Ihor Kharatin's 26th-minute goal in the Basque Country handed the visitors all three points, with Die Alte Dame falling to Brwa Nouri's 22nd-minute penalty in Sweden.
Hertha prop up the group with one point, while Bilbao lie third with an identical record after two outings.
Nice maintained their perfect record in Group K with a 3-0 win over Vitesse at the Allianz Riviera keeping the French club in pole position.
A brace from Alassane Plea (16', 82') helped Les Aiglons to a second successive victory, while Allan Saint-Maximin (45') also got on the scoresheet for the hosts.
Lazio are breathing down their necks, however, after securing a 2-0 victory over Zulte-Waregem at the Stadio Olimpico to make it two wins from two in the group.
Felipe Caicedo gave the hosts an 18th-minute lead, but they had to wait until the 90th minute to seal all three points through Ciro Immobile.
Aleksandr Kokorin struck a brace for Zenit as Real Sociedad slipped to a disappointing 3-1 defeat at Stadion Krestovskyi.
La Real were trailing as early as the fifth minute when Emiliano Rigoni opened the scoring, before Kokorin (24') doubled the hosts' lead.
Diego Llorente (41') halved the deficit for the visitors just before half-time, but Kokorin restored the Lions' two-goal cushion on the hour mark.
Thursday's Europa League results:
Astana 1-1 Slavia Prague
Viktoria Plzen 3-1 Hapoel Be'er Sheva
Lugano 1-2 FCSB
Athletic Bilbao 0-1 Zorya
Ostersunds 1-0 Hertha Berlin
FC Koln 0-1 Red Star Belgrade
BATE 2-4 Arsenal
Red Bull Salzburg 1-0 Marseille
Konyaspor 2-1 Vitoria Guimaraes
Lazio 2-0 Zulte-Waregem
Nice 3-0 Vitesse
Rosenborg 3-1 Vardar
Zenit 3-1 Real Sociedad
Maccabi Tel Aviv 0-0 Villarreal
Partizan 2-3 Dynamo Kyiv
Skenderbeu Korce 1-1 Young Boys
AEK Athens 2-2 Austria Vienna
Milan 3-2 Rijeka
Lyon 1-1 Atalanta
Everton 2-2 Apollon
Ludogorets 2-1 Hoffenheim
Sporting Braga 2-1 Istanbul Basaksehir
Lokomotiv Moscow 3-0 Zlin
Sheriff 0-0 Copenhagen