Spurs fell behind inside 13 minutes to another effort from the in-form Loic Remy, with a leggy first-half display seeing them come off second best.
An improved display after the interval saw them lay siege on the Newcastle penalty area, but the breakthrough proved elusive - with Tim Krul in inspired form for the visitors.
Villas-Boas told Sky Sports after seeing his goal-shy outfit draw another blank: "We gave the first half advantage to Newcastle, although I think we were very unlucky during all of the game.
"We had so many good, good chances that I think the result is very unfair.
"Obviously Newcastle came in strong and really played well in the first half. I think they deserved to get that lead, I think we didn't recognise ourselves in the first half. We were not on top of our game and let ourselves be anticipated a lot. It wasn't one of our better first halves.
"Still we had some good opportunities in the first half, then in the second half if we had been a bit more lucky we could have drawn the game and gone on from there.
"Disappointing because it's not what we deserved. We gave a good response in the second half."
On the performance of Krul, Villas-Boas added: "Last season he had a great game here as well, and today he was the inspiration. He made the difference today."
Sky Sports' Jamie Redknapp agreed that Krul was the main obstacle to Spurs getting a result.
He said on Super Sunday: "I don't think the Europa League was to blame for Tottenham's loss because if it were, how would you produce the second half of football that they did?
"They pretty much battered Newcastle and if it wasn't for Tim Krul they'd have got a result, so no I don't think Europa league is an excuse.
"Tottenham have got a huge squad, they've spent vast amounts of money, I just don't think the team are performing well enough. I think they're over-reliant on Andros Townsend and unless he's going to cut in and score from 25 yards you actually look at Spurs and think - where are they going to open the door? Where's that little bit of imagination that they've had so often?
"It hasn't really happened for Christian Eriksen, does Erik Lamela get a game now? For £30million you expect him to get on the pitch at some stage. Soldado needs the right kind of service and the balance isn't right in the team."
Much of the pre-match talk in north London focused on Hugo Lloris' absence from the Spurs squad, but Villas-Boas insists the situation has been blown out of proportion - with a concussion suffered by the French goalkeeper at Everton no longer an issue.
He said: "It was nothing to do with the situation at Everton. The goalkeeper stayed out because my medical department advised that he wasn't ready, although he is very short on coming back. If the game was tomorrow, he would have played."