Fabian Frei struck late on to ensure Basel reached the quarter-finals.
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Basel booked a quarter-final tie against Shakhtar Donetsk with a comfortable aggregate success against the German side.Basel vs Frankfurt: As it happened
Match in brief
Both sides had chances in the first half with Silvan Widmer denied by Frankfurt goalkeeper Kevin Trapp while Martin Hinteregger and Bas Dost headed over when well-placed for the visitors.
Basel became more dangerous on the counterattack as the visitors pushed forwards after the break with Trapp keeping them at bay several times. Fabian Frei eventually ended the goalkeeper's resistance, though, slaloming through and rounding him to seal the victory.
View from the stadium: Daniel Thacker, Basel reporter
Basel finish the job they began 147 days ago in Germany, victory on the night courtesy of Frei's late strike completing a resounding aggregate triumph. Marcel Koller's side defended resolutely, allowing few clear chances despite mounting Frankfurt pressure as the second leg progressed, and fashioned several good opportunities of their own on the break, Frei finally converting in the closing stages. Shakhtar are next up in Gelsenkirchen, where a similarly stout defensive performance will leave Koller's troops with a good chance of reaching the last four of a European competition for only the second time in club history.
Visitors' view: Jordan Maciel, Frankfurt reporter
It was always going to take something special, but in the end the 3-0 home defeat proved too much of a challenge for Frankfurt to overcome. Kostić aside, Hütter will have expected more from his front men, while the game may have been put to bed sooner were it not for Trapp at the other end. Basel deservedly progress to the last eight after a professional job on the night.
Fabian Frei, Basel midfielder: "My goal wasn't decisive in terms of the tie, but it was very nice on a personal level. We have no reason to hide [ahead of Shakhtar]. We can go in with plenty of confidence. We don't need to say how tough it'll be, that's obvious, but we've shown we can beat big sides."
- Basel have won their last five UEFA Europa League matches – all without conceding a goal.
- The Swiss side have won their last seven home UEFA Europa League matches (including qualifying).
- Basel have scored the first goal in nine of their last ten UEFA Europa League matches.
- Frankfurt have not kept a clean sheet in their last eight UEFA Europa League matches.
- Frankfurt have conceded the first goal in six of their last seven UEFA Europa League matches
Basel: Nikolić; Widmer, Cömert, Alderete, Petretta; Xhaka (Marchand 87), Frei; Stocker (Van Wolfswinkel 66), Campo, Pululu (Van Der Werff 66); Cabral (Ademi 80)
Frankfurt: Trapp; N'Dicka (Hasebe 46), Abraham, Hinteregger, Da Costa (Chandler 67); Kostić, Rode (Ilsanker 66), Kohr; Kamada, Silva (Paciência 46), Dost
Basel face Shakhtar Donetsk in Gelsenkirchen at 21:00 CET on Tuesday for a place in the semi-finals.