The Blues, who ended the game with 10 men following Ashley Cole's late sending off, dominated the second half, but looked set to leave south Wales empty handed thanks to Scott Sinclair's superb first-half volley against his former club.
But Jose Bosingwa found his way into the box in the third of four minutes of stoppage time and saw his driven effort take a wicked deflection off Neil Taylor to nestle in the back of Michel Vorm's net.
And Villas-Boas believed that stroke of fortune was just reward for a second half that saw his side lay siege to the Swansea goal, albeit without crafting much in the way of clear-cut chances.
He said: "I think it was a very different first half to the second, completely different.
"In the second half we were more confident and caused Swansea a lot of problems by pressing high.
"The first half was the opposite, we conceded territory and they found spaces and caused problems. Their goal came during the period when we were starting to do things right, we had plenty of the ball but didn't take our chances.
"The second half was very good, a big effort to improve things, if the goal had come earlier we could have got the second due to the motivation and momentum, but they defended very well.
"The goal was a reward for what the team was doing, but we are unsatisfied because if we had played like this in the first half we would have won the game. We let Swansea have that advantage but we responded in the second 45 minutes."
Cole's sending off, after he picked up a second booking for a sliding challenge on Nathan Dyer, means the England full-back will miss this weekend's crunch clash with Manchester United.
And Villas-Boas admits the loss is a big blow to the Blues, who were without John Terry due to a knee injury, with the England captain's court case into his alleged racial abuse of Anton Ferdinand - which he strenuously denies - set to begin tomorrow.
"His first booking was fair, the second was a more difficult challenge to asses due to the speed it happened at. Ashley thought he was getting the ball and Dyer anticipated but I am not sure there was enough contact (for it to be a booking) as Dyer got up straight away.
"He is one of our key players, Ashley is immense and of course he will be a big loss."
Tottenham's win over Wigan means Chelsea are now seven points adrift of their third-placed London rivals, but Villas-Boas is confident his side can make up that gap.
"The gap was reduced a few weekends ago, so we go back to how we were before, a seven-point gap is nothing in the Premier League. Tottenham are still within our reach and we will see what we can do."
But the Portuguese reiterated that his side are involved in the title race.
He said: "It makes no sense for me to speak about the league, we are competing for the Champions League and that's our main objective.
"To get to first is extremely difficult. We will face the new joint-leaders next weekend and in the aftermath of that game we will see where we are."
Swansea manager Brendan Rodgers felt the result had been cruel on his side as they narrowly avoided a repeat of their stunning success over Arsenal in their previous home game.
He said: "I thought it was a terrific performance, we deserved to win the game.
"We are bitterly disappointed to have conceded right at the end. The players were magnificent, we dominated the game with the ball in the first half and we had good control defensively in the second half.
"We restricted Chelsea's chances and we were just punished late on. I am very proud of the players and to feel that way after drawing with Chelsea is pleasing, but we felt we should have had the three points."
Rodgers also confirmed that he has made a late addition to his squad before the transfer window shuts.
Highly-rated Wrexham defender Curtis Obeng has joined the Swans on a three-and-half year contract for an undisclosed fee, with Daniel Alfei being loaned out to the Dragons for the rest of the season.
Rodgers said: "Curtis Obeng is an excellent talent, he has done well at Wrexham and he fits the bill for us. We wanted to bring in young players that can improve and have that hunger. He has great pace and he has talent."