The news marks the end of a seven-year partnership between Whincup and Paul Dumbrell, while Lowndes has teamed with Steven Richards for the last five seasons.
Triple Eight is yet to confirm a co-driver for Shane van Gisbergen, whose 2018 partner Earl Bamber is unavailable due to a clashing commitment with Porsche.
This year’s PIRTEK Enduro Cup will kick-off with the Supercheap Auto Bathurst 1000 on October 10-13, with the Sandown 500 now after both Bathurst and the Gold Coast 600.
Although not sharing a Supercar since 2009, Lowndes and Whincup won the 2017 Bathurst 12 Hour together in a Ferrari and will again team up for the GT3 classic on February 3.
Together with van Gisbergen, they will drive a Triple Eight-run Mercedes-AMG, backed by Vodafone, which sponsored the Supercars effort from 2007-12.