Villas-Boas' recall of Lampard for the Group E clash was completely justified, with the midfielder scoring what looked set to be the winner at the Mestalla.
But the Chelsea's manager's 83rd-minute substitution of his fellow 33-year-old proved disastrous, with replacement Kalou immediately conceding a needless penalty which saw Roberto Soldado make it 1-1.
Villas-Boas rejected suggestions he should have sent on a more defensive-minded player, with his side under pressure at the time.
"No, no, no, no," he said.
"Putting on a striker is nothing to do with being more offensive or putting on a defender sometimes is nothing to do with being more defensive.
"I think it was the right choice bearing in mind what we were looking at, which was the fact that Valencia were coming out on the left side and doing a lot of two against ones against Bosingwa."
He added: "We controlled the left side. The goal doesn't come from that situation.
"If you bring on a defender, you suffer the goal the same.
"So it's nothing to do with that in my opinion."
The build-up to Wednesday's game was dominated by speculation about Lampard's future after his reduced role in recent weeks and on Tuesday night Villas-Boas declared himself fed up of answering questions about the midfielder.
Lampard arguably benefited from his manager's decision to hold him back for the bigger game and Villas-Boas said: "It was a good performance, a good display from a top player, one of the best players in the squad.
"A goal always comes at a good time for Frank. He's been a goalscorer all his life.
"His abilities are never in doubt and we trust him 100% - like I told you."
Chelsea should have been further than 1-0 ahead before Lampard's substitution as their wastefulness in front of goal returned.
"It was a pity," said Villas-Boas.
"We had very, very good opportunities to reach 2-0 and we just couldn't find the back of the net. It was very, very unlucky.
"The performance was solid and a draw away from home, if it's proposed to you before you take it.
"So near to a win, it leaves you with a strange feeling but we're in a good position still in the group.
"We're looking forward to the Genk game - they're going to be difficult games, of course.
"But if we get six points out of them, we're almost ensured qualification."
Villas-Boas had no complaints with Valencia's penalty and refused to condemn Kalou for conceding it, saying: "I'm not going to criticise him.
"These things sometimes happen in football."
Chelsea's frustration boiled over at the final whistle, which witnessed a flurry of yellow cards after the referee blew for full-time after awarding Chelsea a free-kick.
Villas-Boas said: "We wanted to organise ourselves and that could've been a chance for us.
"But the referee decided to end the game and we reacted a bit to suffering the penalty so late."
Valencia boss Unai Emery was delighted with his players' never-say-die attitude.
"I'm really happy with my players' performance, especially with their attitude on the pitch," he said.
"They've been fighting for every single ball on the pitch tonight against a great team like Chelsea and I believe that it was a fair result in the end.
"We got a point, we had some chance to maybe score more goals but, in the end, a point is good enough for us."
Emery's decision to drop goalkeeper Vincente Guaita and hand Diego Alves his first start of the season proved a masterstroke, with the Brazilian making a succession of stunning saves.
"The good news for Valencia is that we have two fantastic goalkeepers," Emery said.
"After tonight's performance, I'm going to wait a bit until I make my mind up whether I'm going to carry on playing Alves in the Champions League."