Djukic's side prevented Swansea from booking their spot in the last 32 on Thursday after Daniel Parejo's first half strike gave Valencia a 1-0 win at the Liberty Stadium.
The result means Swansea will need at least a draw in their final group match in a fortnight to progress and Djukic has no doubt they are good enough to get through.
The Serbian was also pleased with his side's first half performance in Wales but felt they may have rode their luck after the break to get the result.
"I think Swansea are a great team and I think they will qualify," Djukic said.
"From the beginning I thought both Valencia and Swansea would qualify for the knockout stages and they played well enough.
"Yes I think it was fair of (Swansea manager) Michael Laudrup to say it was one half each in this match. We had a very good first half and played well.
"I think in the second half Swansea came close and we had to defend very well. So yes, I do agree with his comment."
The victory ensures Valencia's progression to the last 32 with a game to spare and is sure to lift the confidence at the Mestalla after a tough run of form in La Liga.
"We've recovered our morale against a team who are far from easy to beat," Djukic said.
"I'm happy for the players, for being top of the group, for the win which gives us peace of mind, for having kept a clean sheet, and for having had a good game.
"It's a fact that in La Liga we're not where we want ourselves to be but in the Europa League, we are."
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