Eric Dier was penalised for handball in stoppage time after Andy Carroll’s header struck his arm from point blank range.
The penalty was given following a VAR check – and scored by Callum Wilson to earned Newcastle an unlikely 1-1 draw.
The decision looked harsh on Spurs and sparked plenty of reaction, with Sky Sports pundit Jamie Carragher calling it an “absolute disgrace” that was “ruining football”.
Vertonghen, who left Tottenham at the end of last season and has since joined Benfica, accused the FA of “hiding behind” referees who are simply following the latest rules and guidelines.
The Belgian defender tweeted: “The FA needs to start asking themselves some serious questions.
“Absolutely shocking decisions and they are hiding behind the referees.”
A similar incident on Saturday saw Everton awarded a penalty in their win over Crystal Palace – a decision that was heavily criticised by Eagles boss Roy Hodgson.
Newcastle boss Steve Bruce said: “I can understand why Spurs will go berserk and Roy Hodgson reacted like he did.
“It is a total nonsense. We should be jumping through hoops but I would be devastated if that was us.”