Gerard Moreno's penalty secured a first-leg win for Villarreal in Zagreb.
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Gerard Moreno continued his fine form with the only goal as Villarreal clinched a narrow victory in Zagreb.
Match in brief
The visitors were always in the ascendancy, although Mislav Oršić had an early goal disallowed for an offside against Iyayi Atiemwen.
However, the balance shifted after Moreno's cross was handled by Kevin Théophile-Catherine and the striker made no mistake from the spot.
Villarreal dominated after the break but were unable to find a second goal to take back to Spain for next week's second leg.
Elvir Islamović, Dinamo Zagreb reporter
Starting without their powerful striker Bruno Petković, Dinamo were focused on defending solidly and hitting on the break. It was going to plan until they conceded the penalty and they never quite recovered. Not fully fit, Petković came on to bring some extra attacking power in the second half, but it was not enough. The difference in class between the sides was obvious and it will be difficult for Dinamo to turn things around in Spain.
Graham Hunter, Villarreal reporter
This was competent. Not massively full of flair, not decisive in who will progress to the semi-finals, but ultra-competent. All over the pitch, the Yellow Submarine squeezed mistakes to the minimum and wherever they found Dinamo to be their equal, they simply switched the tactical probing to another area. I will bet Unai Emery and his players are a surprised at how much time they had on the ball, to pass, pass and pass again. Dinamo, however, cannot be surprised at the name of the winning goalscorer. His penalty confirms it: Gerard Moreno has never been more prolific in his life.
Gerard Moreno, Villarreal goalscorer: "We got the good result we came seeking but Dinamo are a good side and the second leg will be this tough, or perhaps more so, against them. But Villarreal are putting together an inspirational season."
Etienne Capoue, Villarreal midfielder: "We played a good game and scored the goal at the best possible time. In the second half we could have scored another goal or two, as we were dominating. It won't be easier in the second match, it will only be harder as we are only one goal up."
Rasmus Lauritsen, Dinamo Zagreb defender: "We still have 90 minutes in Spain, I believe we can do it, I really believe. That's football, we did it against Tottenham, we showed we can do it, why wouldn't we do it again?"
- Gerard Moreno has scored 16 goals in his last 15 games for Villarreal, and has contributed 14 of the club's last 22 goals.
- Dinamo Zagreb suffered just their third home defeat of the season, having won 17 of the 22 they have played.
- Villarreal have won their last six matches, their best run since December 2014 when, under Marcelino, they managed seven in a row.
- Villarreal have a perfect record of progressing when they have won the first away leg of a UEFA Cup/UEFA Europa League tie: five out of five to date.
Dinamo: Livaković; Ristovski, Lauritsen, Théophile-Catherine, Gvardiol (Leovac 71); Ademi, Jakić (Kastrati 61); Ivanušec, Majer (Franjić 82), Oršić (Tolić 82); Atiemwen (Petković 61)
Villarreal: Rulli; Foyth, Albiol, Pau Torres, Pedraza; Parejo, Capoue, Trigueros (Peña 86); Chukwueze (Moi Gómez 69), Bacca (Alcácer 46), Gerard
Both teams are back in action on Sunday, when Croatian league leaders Dinamo are across town at bottom side Lokomotiva and Villarreal host Osasuna. The second leg then takes place on Thursday, with Arsenal or Slavia Praha awaiting the victors in the semi-finals.