The second generation Vios was made available in four grades for the Malaysian market, namely J, E, G and S.

The J grade is the entry-level, no-frills version of the Vios. It was initially unavailable at the Malaysian Vios launch in October 2007, but was introduced 8 months later on 1 July 2008, offering a choice of either 5-speed manual or 4-speed automatic transmissions and costing between RM69,800 and RM73,500 respectively.[14]

The E grade is considered to be the lower-middle grade, retailing at RM78,700 at launch, whereas the G grade is the upper-middle grade, costing RM84,800 initially. These two grades differ mostly in terms of equipment levels and are mechanically identical, both sharing the 4-speed Super ECT gearbox.[15] Later on 29 June 2011, another variant called the G Limited was introduced at RM89,600, offering a new body kit, 15-inch alloy rims and leather seats on top of those already offered in the G grade.[16]

The S grade is a new addition to the Vios lineage. It featured the highest levels of cosmetic enhancements, including a body kit which encompassed a front bumper spoiler, side skirts, rear skirt and a bootlid spoiler.[15] The interior received a dark grey/black trim treatment, and included an Optitron meter with a multi-information display, as opposed to the E and G grades' conventional backlit display. The S grade was the most expensive Vios variant, costing RM88,100 at launch.[15] Later on 17 June 2009, UMW Toyota launched the new Vios 1.5 TRD Sportivo which effectively replaced the S grade.[17] It featured a new body kit, Enkei rims, various interior trim improvements and an optional sports suspension kit. The Vios TRD Sportivo was updated on 29 June 2011, featuring a new grille, unique alloy rims and leather seats.[16]