Spurs fell behind when Luis Suarez netted just after 20 minutes but Jan Vertonghen edged the North Londoners ahead with a goal late in the first half and another early in the second.
However, a defensive error from Kyle Walker and Hugo Lloris allowed Stewart Downing to equalise before Benoit Assou-Ekotto conceded a penalty which Steven Gerrard converted for the win leaving Villas-Boas to rue what might have been, especially after Gylfi Sigurdsson hit the woodwork at 2-1.
"It’s difficult for us to take. We did ever so well to come back into the game first half and then started brightly the second half," he told reporters.
"I think we had control of the game until we lost it. It was more down to a couple of mistakes rather than to Liverpool’s merit, although they fought very, very hard and pressed us hard and in the end they deserved [a result].
"But it’s a pity that we lost control of the game when things looked to be going our way. Probably the Sigurdsson chance for 3-1 that hits the post could be the moment of the game because that would probably mean three points for us."
He added: "Liverpool pressed us hard on that back-pass that goes from Walker to Lloris and they deserve credit for that, for putting us under pressure really quickly.
"Moments like this can happen and you can’t be negative to the players who did ever so well to make a 12-game unbeaten run. Hopefully this setback can serve as an example to move forward."