The 25-year-old looked to be on his way to White Hart Lane when Porto accepted a £22m bid from the North London outfit.
However, negotiations reportedly hit a stumbling block early on over the player's personal terms.
Villas-Boas said that the two parties had eventually come to an arrangement, but it was too late to be finalised.
"The deal was almost done but there were problems with the contract," the 34-year-old told Sky Sports News. "It was always a difficult deal to complete and we were ready for it not to happen.
"The player terms were agreed a little bit late but I am extremely happy with the amount of players we have."