Reports had suggested that the Serbian was facing the chop if Los Che succumbed to Unai Emery's side following three successive league defeats and a 3-0 humbling against Swansea City in the Europa League.
However, the home side produced a committed performance in front of their own fans to record their second win of the season, lifting themselves to eighth in the table.
It stayed that way until half time, but the visitors emerged from the tunnel a different team after the break and grabbed a deserved equaliser through Kevin Gameiro.
Dukic's men restored their lead in the 72nd minute and it was the Brazilian midfielder once again who found the net, this time with a curling shot from outside the area.
The points were wrapped up when Victor Ruiz looped a header over Beto in the 83rd minute.