Saxo Bank-Tinkoff Bank rider Contador will also race in the Milan-Turin on Wednesday.
The Spaniard only began the season in August following his doping suspension.
Gilbert, who triumphed in the world championship road race last weekend, will also skip the Giro del Piemonte.
The BMC rider won the Lombardia in 2009 and 2010.
"Phil is very motivated to take his first win wearing the rainbow jersey on Saturday in Lombardia," BMC sports director Rik Verbrugghe told Sporza.
"He didn't party for very long, the course suits him and he's fit."