Pochettino's side trailed to Marc Cucurella's early own goal and a Morgan Rogers strike before half-time at Villa Park.
Rather than capitulate as they did in Tuesday's humiliating 5-0 loss at Arsenal, the Blues dug deep to rescue a gritty point thanks to goals from Noni Madueke and Conor Gallagher.
But Chelsea thought they had won it deep into stoppage time when Villa keeper Robin Olsen turned Axel Disasi's effort into his own net, however, to Pochettino's fury, the goal was disallowed for a Benoit Badiashile foul.
"The referee is unbelievable and it's ridiculous. It is difficult to accept," Pochettino said.
"They didn't see a foul on the pitch and then VAR changed the decision of the referee. For me that was a normal challenge.
"It is painful as it has damaged English football. Villa's players and their fans didn't understand why the goal was disallowed.
"For me it damaged a little bit the Premier League. If we want to be the best league in the world it should be protecting the spectacle and the decision."
The draw was a blow to Villa's hopes of holding off Tottenham in the race to qualify for the Champions League via a top-four finish.
Villa are seven points clear of fifth-placed Tottenham, who host Premier League leaders Arsenal on Sunday in the first of three games in hand on Unai Emery's side.
Although Villa, who last finished as high as fourth in 1995-96, remain favourites to clinch the lucrative Champions League berth, they might feel a little nervous if Tottenham win the north London derby.
"We wanted to play Europa League last year and now we have a new challenge which is to play Champions League," Emery said.
"Chelsea today showed the power. But to draw at the end is a very good result. I want more, of course."
The under-fire Pochettino reportedly retains the backing of Chelsea's ninth-placed squad - which has been assembled for over £1 billion - despite a difficult campaign that included an FA Cup semi-final loss to Manchester City last weekend.
They proved that point by refusing to surrender against a Villa team that flew at them in a vibrant start.
