The FA chief spoke in the aftermath of Sunday's heated Manchester derby which saw United defender Rio Ferdinand struck by a coin thrown from the crowd and nine others charged by police in connection with the match.
Images of Ferdinand's bloodied face cut-open just above the eyebrow and City keeper Joe Hart holding back a fan who had invaded the pitch following Robin van Persie's stoppage-time winner to confront Ferdinand have been published around the globe tarnishing what was a thrilling encounter.
"I think it's disturbing that we are seeing a recurrence of these sorts of incidents. We've had some racial abuse issues... we've had things being thrown at players. They are unacceptable and they have to be dealt with severely," Bernstein told Sky Sports.
"In my mind it's for the FA, it's for the whole game of football and for the authorities to work together to deal with this in the most severe manner.
"I believe that if necessary life bans for these people who need to be caught, go to the courts and be banned for life if and when they are found out."
Bernstein said "copy-cat" behaviour had a role to play in crowd trouble.
"It's a difficult social problem. You have something happen and other people tend to copy it," Bernstein said.
"Therefore it's really important that matters are bought to a head and people understand there is no room for this in football at all and we will do everything we can within the FA. I know the rest of football feel the same way to deal with these matters it's a blot on the game.
"It's very disappointing when you think of the millions watching football every week, or being involved in football, to see it being hijacked by these incidences is awful so we have to deal with it in the strongest way we can."
On the incident involving Ferdinand, Bernstein added: "Totally unacceptable and deplorable to see those incidents obviously Rio Ferdinand with blood on his face is absolutely terrible."
City have apologised to the centre-back, who attempted to make light of the incident on Twitter.
"Whoever threw that coin, what a shot! Can't believe it was a copper 2p... could have at least been a £1 coin!," he said.
Greater Manchester Police say they are still working with the Premier League champions to identify who threw the coin.
