Striker Papiss Cisse saw two goals disallowed as Newcastle failed to claim the first-leg lead over Metalist Kharkiv, instead settling for a goalless draw.
Rodrigo Palacio scored twice following his early entrance as a substitute to put Inter Milan in control of their tie against Cluj.
Palacio, a 10th-minute replacement after a serious-looking injury to Diego Milito, scored 10 minutes after that and added a late second in a 2-0 win.
Anzhi Makhachkala recovered from a goal down to defeat Hannover 3-1 although the Russian side will hope they will not be made to rue Samuel Eto'o's missed second-half penalty.
Hannover took a 22nd-minute lead through Szabolcs Huszti but Eto'o drew Anzhi level soon after and Odil Ahmedov put the hosts ahead immediately after half-time.
Eto'o then spurned the chance to make it 3-1 in the 57th minute when his spot-kick was saved by Ron-Robert Zieler, but Anzhi were still able to secure a two-goal lead to take to Germany for the second leg thanks to Mbark Boussoufa.
Viktoria Plzen confirmed themselves as one of the dark horses in this year's Europa League after shocking Napoli 3-0 in the first leg of the last-32 tie at San Paolo on Thursday night.
Plzen beat defending champions Atletico Madrid to top their group and are now heavy favourites to progress past the high-flying Italians after late goals from Stanislav Tecl and Frantisek Rajtoral built on Vladimar Darida's first-half opener.
Liverpool conceded two goals in less than three minutes to Zenit St Petersburg to leave their Europa League campaign hanging in the balance.
Despite having failed to properly test goalkeeper Vyacheslav Malafeev with a number of chances the Reds seemed to be managing to hold on in the sub-zero Petrovsky Stadium.
But with 20 minutes remaining Hulk powered home a brilliant 30-yard strike before substitute Sergei Semak converted from close range moments later.
Levante put aside their poor domestic form to claim an impressive 3-0 victory over 10-man Olympiacos that leaves them within touching distance of a place in the last 16.
The Spanish outfit out had lost five of their last six in league and cup prior to Thursday night but goals from Pedro Rios, Jose Barkero and Obafemi Martins earned Juan Ignacio Martinez's men a notable scalp against a side who were playing in the Champions League group stages before Christmas.
Oleg Gusev missed a second-half penalty as wasteful Dynamo Kiev played out a 1-1 draw with Bordeaux.
The Ukrainian hosts dominated the contest and took a deserved lead through Lukman Haruna, but that was cancelled out within minutes by Ludovic Obraniak.
Goals by Toby Alderweireld and Ricardo Van Rhijn guided Ajax to a 2-0 victory over 10-man Steaua Bucharest at the Amsterdam ArenA.
Oscar saved Chelsea, interim boss Rafael Benitez and striker Fernando Torres from embarrassment with an 82nd-minute winner at Sparta Prague.
Oscar Cardozo's second-half strike was enough to ensure Benfica will take a slender advantage back to the Estadio da Luz against Bayer Leverkusen.
Meanwhile, Fenerbahce held BATE Borisov to a goalless draw in their Europa League first leg in Belarus despite playing all bar the first three minutes with 10 men after Raul Meireles was sent off early on.
Two goals for Lazio from Libor Kozak as well as three penalties for Borussia Monchengladbach saw a breathless match end with the 10-man Italian club in pole position ahead of the second leg.
Martin Stranzl's penalty put the Bundesliga side ahead before Sergio Floccari and Kozak turned the pendulum Lazio's way.
Stranzl then missed his second penalty, which also saw Andre Dias dismissed following his second yellow card, before three goals in six minutes brought a pulsating 3-3 draw to an end.
Atletico Madrid look to be heading out after they were beaten 2-0 at home by Rubin Kazan.
Gokdeniz Karadeniz put the Russians ahead after six minutes before Pablo Orbaiz doubled their advantage in added on time.
Juande Ramos' chances of becoming only the second manager to win the Europa League for a third time may have to wait another year after his Dnipro side were beaten 2-0 by Basel at St. Jakob-Park.
Ramos had won the trophy twice before at Sevilla and a third triumph would put him level with Republic of Ireland boss Giovanni Trapattoni.
However a first-half goal from Valentin Stocker and a second-half strike from Marco Streller ensured the Swiss side head into next week's second leg at the Dnipro Stadium in control.
Gareth Bale scored two sensational free-kicks as Tottenham gained the advantage over Lyon with a thrilling last-gasp 2-1 win at White Hart Lane.
Samuel Umtiti looked like he had earned a draw for Lyon when he smashed home a stunning half-volley equaliser in the 55th minute, but once again Bale came to the rescue for Spurs.
A last-minute goal from Glynor Plet gave Genk a precious away goal as they held Stuttgart 1-1 at the Mercedes-Benz Arena.
Christian Gentner had fired the hosts ahead before half-time, but Plet struck in stoppage time to level the scores and give his team the advantage heading into the return match in Belgium next week.
Thursday's Europa League Last-32 first leg results