Gareth Bale's tremendous late strike ensured that Spurs would finish with 72 points, their highest ever tally in the Premier League, but they were relying on Arsenal to slip up at Newcastle United to seal UEFA Champions League qualification and that did not happen.
Villas-Boas believes the other top teams have pushed on this season and challenged his side after the clash with Sunderland to respond next term.
He told Sky Sports: "It is a bit disappointing obviously but it did not depend on us and Arsenal did their job to sneak fourth spot."
Asked how he would look at the season as a whole, Villas-Boas replied: "I think very good.
"To manage so many points and not make it means the level has come up, and it serves a reference for next season.
"Others have pushed on a level and next year we have to improve, so it is a good lesson to take into next season.
"It is a pity we missed it this season, because normally it would be enough to qualify."
Villas-Boas was unhappy that Tottenham had not been given a penalty midway through the first half, when referee Andre Marriner instead booked Bale for diving after he had been sent tumbling to the ground by Sebastian Larsson.
Villas-Boas thinks that such an early goal may have had an effect on Arsenal's clash with Newcastle, which ended 1-0 to the Gunners after Laurent Koscielny scored in the 52nd minute.
He explained: "It is very disappointing because a penalty not only changes the running of this game but it also changes the running of the other game too."