A goal by Radamel Falcao in the 84th minute gave the visitors hope of overturning the two-goal deficit from the first leg at the Vicente Calderon last week.
Yet despite playing with a man extra in the final minutes after Rubin captain Cesar Navas was sent off, the Spanish side were unable to score again.
Tottenham reached the last 16 in dramatic fashion as Mousa Dembele popped up with a stunning last-minute strike to secure a 1-1 draw at Lyon and a 3-2 win on aggregate.
Maxime Gonalons looked to have fired Lyon to the 1-0 win they required to advance in the first half, but Dembele scored in the final minute , hammering a 25-yard strike past Remy Vercoutre to set up a meeting with Inter Milan in the next round.
Inter progressed courtesy of a 5-0 aggregate win over Romanian side Cluj.
Fredy Guarin scored twice and Marco Benassi added a late third as the Italians comfortably added to their 2-0 lead from the first leg.
Cluj were forced to play the closing minutes with 10 men following Mario Camora's dismissal.
Shola Ameobi fired Newcastle through from the penalty spot as the Magpies did just enough to see off Metalist Kharkiv in Ukraine.
Ameobi's 15th European goal came after midfielder Moussa Sissoko had been tripped by goalkeeper Olexandr Goryainov and secured a 1-0 aggregate win after the first leg at St James' Park had ended goalless.
Stuttgart eased into the last 16 with a 2-0 victory at Genk.
With the tie delicately poised at 1-1 following the first leg in Germany, goals from Arthur Boka and Christian Gentner saw the Bundesliga side through.
Basle are also safely into the next stage after a 3-1 aggregate win at Dnipro.
In an entertaining match, both teams netted late penalties and finished with 10 men but it was the Swiss visitors celebrating at the end of a 1-1 stalemate.
Trailing 2-0 from the first leg, Dnipro's hopes took a further nosedive when substitute Nikola Kalinic was sent off in the 63rd minute.
The hosts were handed a lifeline 14 minutes from time when Basle midfielder Fabian Frei handled inside the area, earning him an early bath and the home side a penalty from which Yevhen Seleznyov scored.
But five minutes later Basle's 10 men won a penalty of their own and Fabian Schar converted an away goal that killed off the tie.
Lazio comfortably progressed as first-half goals from Antonio Candreva and Alvaro Gonzalez downed Borussia Monchengladbach 2-0 for a 5-3 aggregate win.
Candreva sidefooted the hosts in front inside 10 minutes and Gonzalez's goal shortly after the half hour was enough to seal a routine win.
Viktoria Plzen beat Serie A title hopefuls Napoli for the second time in a week to book their place in the last 16 of the Europa League for the first time.
Plzen cantered to a 3-0 win in Naples last week and they completed a professional performance over two legs with a 2-0 victory tonight thanks to strikes by Jan Kovarik and Stanislav Tecl.
Next up for Plzen is Fenerbahce, for whom Cristian Baroni's first-half penalty was enough see off 10-man BATE Borisov 1-0.
With the scores goalless after the first leg, BATE's hopes were hit by the dismissal of Dmitri Baga, while Cristian's spot-kick was enough to see Fener scrape through.
A Jamie Carragher error proved costly as Liverpool were edged out of the competition on away goals despite a 3-1 win on the night against Zenit St Petersburg.
The veteran defender, making his 150th - and now last - European appearance, gifted Zenit's star forward Hulk a goal that gave the Russians a 3-0 aggregate lead.
Liverpool responded as top scorer Luis Suarez fired in two free-kicks and Joe Allen struck from close range but Hulk's away goal was decisive as the tie ended 3-3.
Substitute Eden Hazard saved Chelsea's blushes as his late goal secured a 1-1 home draw with Sparta Prague and a 2-1 aggregate win.
Hazard netted in the final moments of the contest after David Lafata had earlier wiped out Chelsea's first-leg advantage as he fired in from close range after 17 minutes.
Benfica saw off Bayer Leverkusen 3-1 on aggregate in their encounter in Portugal.
Benfica held a 1-0 lead from the first leg in Germany thanks to Oscar Cardozo's goal, and their lead was doubled when Ola John found the net after an hour.
Andre Schurrle equalised for Leverkusen on the night with 15 minutes to go, but Benfica restored their two-goal cushion two minutes later through Nemanja Matic.
Benfica next play Bordeaux who progressed after a 2-1 aggregate win over Dynamo Kiev.
A solitary goal by Cheick Diabate shortly before half-time was enough to guide Bordeaux through after the first leg in Ukraine ended 1-1.
Anzhi Makhachkala set up a last 16 tie with Newcastle despite a 1-0 loss at Hannover.
Trailing 3-1 from the first leg, Hannover threw everything they had at the Russians but only had Sergio Pinto's 70th-minute goal to show for it as Anzhi squeaked through.
Levante are through to a tie with Rubin Kazan after a 1-0 win at Olympiacos.
The Spanish side held a 3-0 lead after the first leg and duly wrapped up a 4-0 aggregate win thanks to Obafemi Martins' early strike.
Steaua Bucharest marched through against Ajax with a 4-2 win on penalties after fighting back from 2-0 down from the first leg. Goals from Iasmin Latovlevici and Vlad Chiriches took the tie to extra-time and penalties ensued with the hosts progressing with Latovlevici scoring the deciding spot-kick.
EUROPA LEAGUE LAST 16:
Anzhi Makhachkala v Newcastle
Basle v Zenit St Petersburg
Benfica v Bordeaux
Levante v Rubin Kazan
Steaua Bucharest v Chelsea
Stuttgart v Lazio
Tottenham v Inter Milan
Viktoria Plzen v Fenerbahce
Matches to be played March 7 and 14.
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