"Lennon won't be able to make [the England games]," Villas-Boas said. "He has been struggling a lot with injuries.
"We risked him the other day against Inter Milan and he is on the brink of rupturing his muscle so we have decided to take him out of this game. He has groin and hamstring [injuries]."
Villas-Boas also said that centre-back Michael Dawson was unlikely to be able to join up with the squad because of a hamstring injury.
Roy Hodgson's side face San Marino on Friday before taking on main contenders for first place in the group, Montenegro, on Tuesday.