Los Che booked their place in the knockout stages of the Europa league on Thursday night with a 1-0 win at Swansea.
Dani Parejo scored the only goal on 20 minutes to tie up a fourth win on the spin in Europe.
By contrast Djukic's side have won just once in their past seven Primera Division games, which has left the Serbian coach under some pressure.
"We are very happy especially in this situation," said Djukic.
"We needed a win to get our confidence back.
"We need to learn how to suffer in games, we played a very good team who came at us in the second half and we coped well."
Djukic perhaps needed the result personally after an unsettling few days following the appointment of sporting director Francisco Rufete.
One of Rufete's first moves has been to start recording the Serbian's training sessions, but Djukic was not taking centre stage after the match.
"I am very happy for the players and everyone at the club," he said.
"I'm happy for the players because we have finished first in the group, for the win that allows us to relax, for keeping a clean sheet and for having played a good match."