The 2006 model year brings more changes for Saab's 9-3 lineup. Six distinct models will continue to wear the 9-3 badge, but new a new trim and body style debut this year. The Lear and Arc names have been dropped and replaced by a single 2.0T style, which is available with both the sedan and convertible bodies. A new wagon model, called the SportCombi, also arrives in 2006. The upscale aero trim returns, and it is now powered by a new V-6 engine. The Aero's previous 210 horsepower mill now powers the 2.0T, and the 175 horsepower engine had been discontinued.

The 2.0T sedans and convertibles are powered by the familiar 2.0 liter turbocharged inline four, which generates 210 horsepower and 221 pound-feet of torque. A five-speed manual transmission is standard on the 2.0T models, and a five-speed automatic transmission is optional. The Aero models house a new 2.8 liter V-6. This potent engine delivers 250 horsepower and 258 pound-feet of torque, and comes with a six-speed manual transmission. Aero buyers may also upgrade to a new six-speed automatic. The V-6 fuel economy is estimated at 18/28 mpg with the manual and 17/28 with the automatic.

There are four non-wagon models available this year: the Aero sedan and convertible, and the 2.0T sedan and convertible. Both styles are well-stocked with standard luxury features, with the Aero set apart by a few performance and appearance upgrades.

Owners and reviewers have continued to warn about the 9-3's questionable build quality. The interior is laden with plastic pieces, including flimsy dash-mounted cup holders. The "premium" audio system produces a very average sound, and other electronics (windows, sunroof, warning lights) are also reported to be a bit unreliable. The 9-3's unique styling continues to be a strong selling point, along with the abundant cargo space, fuel economy and overall ride comfort.