Dundalk's Europa League Group D rivals Maccabi Tel-Aviv and AZ Alkmaar played out a goalless draw in Israel, meaning the Lilywhites remained in second place in the table.
Zenit’s defeat of Stephen Kenny's men ensured they move on to the knockout stages as group winners but the battle for second is very much on.
There was nothing to separate the sides in Tel Aviv in a cagey encounter, and Alkmaar will now head to Tallaght in three weeks' time for a huge collision with the Airtricity Premier Division champions.
Athletic Bilbao striker Aritz Aduriz netted a hat-trick of penalties, the last in stoppage-time, to complete a remarkable five-goal haul which saw off Genk 5-3 to open up the qualification race in Group F.
Sassuolo remain top after they drew 2-2 at home against Rapid Vienna, who scored a late equaliser - but now all four teams are separated by just one point.
Anderlecht thumped Mainz 6-1 in Group C, where French team St Etienne continued their qualification push with a 2-1 win at pointless Qabala.
Roma won 4-2 at Austria Vienna with a brace from Edin Dzeko to climb to the top of Group E, with the other tie ending 1-1 between Astra Giurgiu and Viktoria Plzen.
Shakhtar Donetsk ran out 5-3 winners at Gent to secure a place in the next stage as Group H winners.
Sporting Braga beat Konyaspor 3-1 in a match which saw both sides have a player sent off.
Ajax also made sure of qualification from Group G with a 3-2 win over Celta Vigo in Amsterdam, holding off a late resurgence from the Spaniards, who are now level with Standard Liege after their 3-0 win at Panathinaikos.
Apoel Nicosia lead Group B after the Cypriots beat Swiss side Young Boys 1-0 and Olympiakos drew 1-1 away to FC Astana.
Schalke are through to the knockout stages after a 2-0 win over Krasnodar left the Germans six points clear at the top of Group I, while Red Bull Salzburg kept their hopes alive after winning 2-0 at Nice.
Fiorentina beat Slovan Liberec 3-0 to top Group J, and Qarabag secured a 1-0 win at PAOK Salonika.
In Group L, Turkish side Osmanlispor moved ahead of Villarreal at the top with a 2-1 win at El Madrigal, while Zurich and Steaua Bucurest playing out a goalless draw.
