UEFA Cup holders Zenit St Petersburg were knocked out at the last-16 stage by Udinese on Thursday while Hamburg SV stunned Galatasaray to deny the Istanbul side the chance of a May final in their home city.
Zenit, 2-0 down from the first leg in Italy, could only win the return match 1-0 at the Petrovsky stadium to bow out 2-1 on aggregate.
Galatasaray appeared to be heading through after taking a 2-0 lead at their Ali Sami Yen stadium following a 1-1 draw in Hamburg.
However, the Bundesliga side roared back with three second-half goals to put out the 2000 winners and end their dreams of reaching the final to be staged at the home of their fierce rivals Fenerbahce.
The last UEFA Cup final before the competition becomes the Europa League next season will have a new name on the trophy after 2005 winners CSKA Moscow were eliminated by Shakhtar Donetsk.
Ukraine will have two sides in the quarter-finals after Dynamo Kiev ousted compatriots Metalist Kharkiv on away goals while Paris St Germain and Manchester City also qualified.
Udinese, 12th in Serie A, are the only remaining Italian side left in Europe this season after AC Milan's demise in the previous round and the exit of Inter Milan and AS Roma from the Champions League.
The Italians were forced on to the back foot by Zenit who enjoyed the majority of possession but failed to add to a 34th-minute goal from Ukraine midfielder and Zenit captain Anatoliy Tymoshchuk who headed in Victor Fayzulin's corner.
Peru striker Paolo Guerrero's quickfire double just before the hour cancelled out goals from Harry Kewell (penalty) and Milan Baros for Galatasaray.
Croatian Ivica Olic then won the game for Hamburg in the final minute by slotting in a David Jarolim through ball.
Shakhtar had two of their Brazilian contingent to thank for firing them into the last eight at the expense of CSKA, who they beat 2-0 at home for a 2-1 aggregate victory.
Attacking midfielder Fernandinho thumped in a 54th-minute penalty after being fouled by Pavel Mamaev and Luiz Adriano turned the tie in Shakhtar's favour with a near-post finish with 20 minutes remaining.
City let a 2-0 first-leg lead slip in Denmark as late goals from Luton Shelton and Michael Jakobsen sent their clash with AaB Aalborg into extra time.
There were no further goals but City progressed after winning the shootout 4-3 with keeper Shay Given saving two penalties.
Striker Guillaume Hoarau hit an 81st-minute winner for PSG against Braga in Portugal, the only goal of the two legs.
An own goal 11 minutes from time secured Dynamo's place in Friday's quarter-final draw as they lost 3-2 at Kharkiv but still went through on away goals.
Werder Bremen and Olympique Marseille also qualified for the quarter-finals on Wednesday.