For 2006, two additional colors were added to the GTO line, Spice Red Metallic and Brazen Orange Metallic, while Midnight Blue Metallic and Yellow Jacket were dropped. Changes for 2006 included revised blacked-out tail lamps, illuminated steering wheel radio controls, faster moving power seat motors, and an interior power door lock switch. The climate control button for the A/C also had the word "Defog" added to it as well. The 2006 GTO was still equipped with the 400 HP 6.0 L engine.

On February 21, 2006, Buick-Pontiac-GMC General Manager John Larson announced to dealers that GM would halt imports of the GTO in September, making 2006 the last model year for the new GTO. The explanation was the inability to meet new airbag deployment standards for 2007. The final production numbers of the 2006 Pontiac GTO were 13,948 units, an increase from 11,069 from the previous model year.

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