In the night's other last 16 tie, Borussia Dortmund beat Shakhtar Donetsk 3-0 to progress 5-2 on aggregate.
Portugal will meet the winner of Saturday's Spain-France quarterfinal Wednesday in Donetsk, Ukraine.
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One of the venues is being funded by Ukraine's richest man, the football-mad billionaire Rinat Akhmetov, for his team Shakhtar Donetsk.
Jeff United defender Zeljko Milinovic was replaced with Shakhtar Donetsk's Muamer Vugdalic and Olimpija's Senad Tiganj came in instead of Cimerotic.
Holders Shakhtar Donetsk took control of Group J with a resounding 4-1 victory over an outclassed Partizan Belgrade at the Olympyiskyi Stadium.
Diego pulled one back after 31 minutes for Bremen who looked weary from their extra-time defeat to Shakhtar Donetsk on Wednesday night.
However he did not received this money from a publisher but an unknown printer in his hometown of Donetsk in eastern Ukraine.
The clash pairs two of the favourites for the competition, with Sevilla pulling off a remarkable escape to go through against Shakhtar Donetsk.
BBC: SPORT | Football | Europe | Tottenham face tough Sevilla test
Samir Nasri rescued a point for France in Donetsk after his Manchester City team-mate Joleon Lescott had fired England into a first-half lead.
The east's suspicions were sharpened by the arrest in April of Boris Kolesnikov over the allegedly violent takeover of a Donetsk department store.
That's exactly what he did in 2007, when Corinthians ignored overtures from Europe's traditional powers and instead sold him to Ukraine's Shakthar Donetsk.
Shakhtar Donetsk, Juventus and Hamburg have all been beaten by Fulham en route to the final, with Spain's Atletico Madrid now standing in their way.
"He's not played with us or practised with the group, so I'm quite surprised he's in, " said Wenger after Arsenal's 2-1 defeat by Shakhtar Donetsk.
Arsenal will play Shakhtar Donetsk, Braga, Partizan Belgrade in Group H.
The success continues a sensational second European campaign for Fulham, who had eliminated defending champions Shakhtar Donetsk and favourites Juventus in the previous two rounds.
Both nations will provide four venues, with the final to be played in the Ukrainian capital of Kiev and other matches in Donetsk, Lviv and Kharkiv.
The match will be the last in a continental campaign that has included victories over defending champions Shaktar Donetsk and Italian giants Juventus for Hodgson's side.
They have since eliminated defending champions Shakhtar Donetsk, favourites Juventus and Wolfsburg in the knockout stages, with Thursday's victory their 16th match in the competition this season.
Petersburg, Portuguese champions Porto and Ukrainian title winners Shakhtar Donetsk -- three teams who have all tasted glory in the second-tier Europa League in the last four years.
Adding to their discomfort, the English players will be sprayed with insect repellent before the game to combat swarms of airborne bugs, that are a feature of Donetsk in the summertime.
The German hopes flew to Istanbul for Wednesday's UEFA Cup showdown with Shakhtar Donetsk desperate to make up for a disappointing domestic league campaign with Bremen destined to finish in 10th place.
Defending champions Shakhtar Donetsk moved five points clear in Group J , with the Ukrainian side winning their third successive game and scoring four goals for the third time, crushing Toulouse 4-0.
Wenger hopes captain Fabregas will be fit to travel to Donetsk and revealing the Spaniard may have suffered a recurrence of the hamstring injury that recently kept him out for a month.
They completed the formalities in Donetsk after a scintillating performance at the Camp Nou six days ago that had all but secured their progression into the last four for a fourth successive season.
And while the victories over Shakhtar Donetsk, Juventus and Wolfsburg made the wider football world take note, it was those unheralded early travels that laid the groundwork for the drama that was to follow.
Fulham have won plaudits this season for their performances in the Europa League, which has seen them claim impressive results against Basle and Roma and knock out holders Shakhtar Donetsk in the last 32.
Donetsk Governor Andrei Shishatsky said that rescuers had located one of the missing people in the wreckage of the plane but were still unsure whether the person was alive, the Interfax news agency reported.
While Rooney isn't renowned for his picturesque passes in the same way that David Beckham was, there is evidence to suggest his return will have a significant impact on England's ability to retain possession in Donetsk.
However, if Shakhtar Donetsk avoid defeat, Arsenal would only be able to finish second at best and would face a group winner if they qualify - and so could face the likes of Real Madrid or Barcelona.
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Having handed a first start to Bolivian striker Marcelo Moreno, a deadline day loan signing from Shakhtar Donetsk, Wigan had a focal point for their attack, with Rodallega cutting in from the left and N'Zogbia from the right.
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