The Portuguese tactician was left with a bad taste in the mouth after seeing his side miss out on victory when they were minutes away from securing complete control of Group E
Frank Lampard had initially put the Blues in front around the hour mark, and they could have moved further ahead but for the fine interventions of Diego Alves in the Valencia goal.
Speaking after the match, Villas-Boas said he believed their performance merited three points and that the result was tough to take when Chelsea were so close to securing a commanding advantage in Group E.
"It was a pity to concede the late goal because I thought we had been looking very good to pick up the three points," Villas-Boas told Sky Sports.
"So it was a pity to suffer a penalty that condemns a little bit what had previously been a very good performance by the team.
"I’m very happy with the display form everybody and before the game if you are offered a draw in Valencia then maybe you take it but to be so near to winning the game and be in such a good position to qualify with the two Genk games we have to come leaves us with a feeling we do not like.
"Even so, after it went to 1-1 we managed to find ourselves in front of goal [with the Anelka chance] but still couldn’t find the back of the net to give us the 2-1 situation. I think it would have been more deserved for us to win this game."
Lampard was in fine form for Chelsea, scoring one and setting up multiple goalscoring opportunities for his team-mates which they failed to take, but Villas-Boas wasn't in the mood to talk about his midfielder after continuous speculation surrounding his role in the team after his recent demotion to the substitutes' bench.
The Stamford Bridge boss continued: "It was a strong, solid performance from the team, we just need to find that prolificness in front of goal, eventually when that comes we can get more solid results and get to two-goal advantages earlier on in matches.
"Lampard played well, as did the rest of the team, it was a good solid performance but he has been playing well in the rest of the games too, so there’s no speculation and I have nothing else to say on that really."
Villas-Boas also spoke about the penalty decision which cost his side a point and did not blame the referee, but did point out that Fernando Torres had been brought down early in the first half and could arguably have had a penalty himself.
"It is useless and pointless to talk about the referee's performance now after the match, if he decides theirs is a penalty then it is a penalty," he said.
"But apparently there could have been a penalty given for the foul on Fernando Torres in the first half. Ultimately the referee’s decisions are nothing to do with Chelsea."
Villas-Boas was then asked about the contribution of his goalkeeper Petr Cech, who had a good outing, but he instead chose to praise Valencia's Diego Alves for making a string of outstanding saves, saying he was the shot stopper who had the most influence on the end result.
"Cech made a solid contribution but it was not as significant as Diego Alves’ for Valencia," he said.
"Petr was always present and correct, but their opportunities were not as good as the ones we had.
"I think Diego in the end had four fantastic saves right in front of our players one against one which decided the result of the game, so if you are going to praise a goalkeeper for deciding the result of the game then it should be Diego."