Vernazza, who had been booked three minutes earlier for ungentlemanly conduct, ran to challenge Burnley's David May. The defender fell to the ground and the referee promptly showed the midfielder a second yellow.
"The referee must have been able to see that Paulo pulled out of the challenge. If he had gone through with it then it would have been understandable," said Lewington.
The Watford manager was also unhappy with the referee's decision to award Burnley a 31st minute penalty that Robbie Blake contrived to miss after sending keeper Alec Chamberlain the wrong way.
"The ball was driven at a ferocious pace from ten yards straight at the player's face. He raised his hand to protect his face. That is only natural," added Lewington.
It looked as though it might work out well for the struggling home side when they took a deserved lead seconds before the interval.
A Neal Ardley free-kick was nodded down by Watford skipper Neil Cox and Scott Fitzgerald claimed his third goal of the season with a diving header.
"We were below our normal standard in the first half and Watford deserved to go ahead, " said Burnley boss Stan Ternent.
Burnley broke back eight minutes into the second half. A Gareth Farrelly long throw was nodded away by Watford defender Marcus Gayle but straight into the path of Luke Chadwick. His shot took a deflection off defender Paul Robinson and bounced up into the net.
Watford had a penalty appeal turned down when Bruce Dyer was felled in the box and there was an angry confrontation between Ardley and May.
After Watford were reduced to ten men Gavin Mahon tested the Burnley keeper with a shot and Danny Webber had another attempt deflected over the bar.
Despite having the extra man Burnley made hard work of trying to break down the Watford defence until a late mistake by Mahon set up Chadwick for a shot which hit the inside of a post before Mahon cleared.
Watford: Chamberlain, Kelly, Cox, Gayle, Robinson, Ardley, Vernazza, Mahon, Fitzgerald, Webber, Dyer. Subs: Dyche, Hand, Cook, Young, Pidgeley.
Burnley: Jensen, West, Todd, May, Camara, Ian Moore, Farrelly, Weller, Chadwick, Blake, Facey. Subs: Roche, Branch, Chaplow, O'Neill.
Referee: A Hall (West Midlands).