Feeney led into the final three minutes of the session, before Boys fired his Image Racing entry to the top with a 2:06.502s.
At the death, Mouzouris dropped in a 2:06.199s to put over three tenths on the field.
As the chequered flag fell, Everingham rose from 10th to third, with teammate and Practice 1 fast man Jayden Ojeda slotting into fifth.
Feeney, who was on a purple first sector, had a bobble at the final corner and couldn't improve, falling just short of a maiden pole position of his own.
Eggleston Motorsport's Matthew McLean impressed in his Super2 debut to clinch fifth on the grid, pipping Ojeda.
Josh Fife and Zak Best filled out the fourth row, ahead of Aaron Seton and Matt Chahda.
The Dunlop Series will return to the track at 1:40pm AEDT for Race 1.