Lampard was already a doubt with a knee injury which has now seen him sidelined, while Bertrand is suffering from a sore throat. Both have returned to their club for further treatment, but will rejoin Hodgson's squad at the weekend to see if they will have recovered in time for England's tricky away encounter against Poland in Warsaw.
A statement on the FA's official website stated: "Frank Lampard has returned to his club for further treatment and will not be available for England's FIFA World Cup qualifier with San Marino.
"Ryan Bertrand has also returned to Stamford Bridge with illness. The defender will also return on Sunday to be assessed ahead of the Poland game."