Thomas is focussing on stage racing this season, racing at the Volta a Catalunya this week instead, with Stannard and Rowe entrusted to follow the Welshman's good work on the cobbles in 2015.
Last year's Amstel Gold Race winner and 2014 World Champion Michal Kwiatkowski starts E3 Harelbeke, but sits out of the sprinter Classic, Ghent-Wevelgem on Easter Sunday.
Your essential guide to the cobbled Classics
Andy Fenn, Michal Golas, Christian Knees, Salvatore Puccio and Elia Viviani join Stannard and Rowe in riding both races over the weekend, with Danny van Poppel replacing Kwiatkowski on Sunday.
Sky also announced that Mikel Landa will make his debut for the team at the Settimana Coppi e Bartali in Italy between March 24-27. The Basque rider has been absent with illness so far this year and is looking to gain form and fitness ahead of the Giro d'Italia.
According to the Sky website, van Poppel will also ride Coppi e Bartali, despite it clashing with Ghent-Wevelgem on Sunday.
Team Sky squads
E3 Harelbeke: Andy Fenn, Michal Golas, Christian Knees, Michal Kwiatkowski, Salvatore Puccio, Luke Rowe, Ian Stannard, Elia Viviani
Ghent Wevelgem: Andy Fenn, Michal Golas, Christian Knees, Salvatore Puccio, Luke Rowe, Ian Stannard, Elia Viviani, Danny van Poppel
Coppi e Bartali: Philip Deignan, Sebastian Henao, Mikel Landa, David Lopez, Gianni Moscon, Alex Peters, Danny van Poppel, Xabier Zandio
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