It was the Gunners first defeat of 2003 and Blackburn become only the second Premiership team to shut their forward line out since May 2001.
It was more than deserved as Rovers took full advantage of their two weeks off, in stark contrast to Arsenals packed fixture list.
Injuries robbed the Gunners of Patrick Vieira, David Seaman and Sol Campbell while Martin Keown limped off early on.
However, the home team were also denied key players such as David Dunn, David Thompson and Lucas Neill.
Star winger Damien Duff though did make a return to action after almost two months out through injury and he scored the opening goal - at the third time of asking.
A cross from the right was miscued by Duff to Tugay. His shot hit Dwight Yorke and rebounded into the air but as the ball dropped there was Duff to hammer into the bottom corner.
Earlier, Thierry Henry had forced a top-class save from Brad Friedel, Blackburns star performer in this increasingly productive season.
After Robert Pires had missed a golden headed opportunity just before the break, the home team made it two in the 52nd minute.
Tugay advanced unchallenged from the centre circle before unleashing a wicked drive that bent round Stuart Taylor into the far corner. It was the impressive Turks first goal of the season.
Blackburn boss Graeme Souness was delighted with his sides overall performance saying; "We were determined to give Arsenal a difficult game today, we were up for it.
"We deserved to win.
"Arsenal manager Arsene Wenger on the other hand stated tiredness as a key reason for his sides defeat: "We didn't have the legs to win this game, he remarked.
"We lost too many of the 50-50 battles. We deserved to lose and we lost."
Blackburn: Friedel, Taylor, Berg, Short, Gresko, Gillespie, Flitcroft, Tugay, Duff (Johansson 69), Sukur, Yorke (Gallagher 78).
Subs Not Used: Grabbi, Douglas, Kelly.
Booked: Duff, Tugay, Flitcroft, Sukur.
Arsenal: Taylor, Lauren, Keown (Silva 18), Cygan, van Bronckhorst, Pires (Wiltord 69), Parlour, Edu (Jeffers 69), Ljungberg, Bergkamp, Henry.
Subs Not Used: Toure, Warmuz.
Booked: Parlour, van Bronckhorst.
Attendance: 29,840
Referee: S Bennett (Kent).