Caulker, who was included in Hodgson's squad to face Italy in August, has played in four of Tottenham's last five matches, moving ahead of club captain Michael Dawson in the pecking order.
The 20-year-old also impressed at this summer's Olympics, and Villas-Boas believes that it is just a matter of time until he makes his England debut.
"I think for Steven it will be a privilege to play for the first team of England, for sure," said Villas-Boas.
"If it came sooner it would be a more important achievement, but I don't see [him being left out] as any kind of negative. We certainly believe a lot in the player. That's why we decided to extend his career and that's why he played at Old Trafford and against Lazio.
"I think he is showing exactly the competence and the talent that he has and he will triumph in the future."
Hodgson opted for Stoke City's Ryan Shawcross ahead of Caulker for the matches against San Marino and Poland on October 12 and 16 respectively.