Alli's decider came early on, during a frantic first twenty minutes, in which Jan Vertoghen had put Spurs ahead before Joselu levelled less than three minutes later.
Spurs had nine players reach the last four of the World Cup, yet five of them, who had only resumed training on Monday, were fast-tracked into Mauricio Pochettino's starting line-up as the Spurs boss rolled the dice at St. James' Park.
Among them were England skipper Harry Kane, World Cup winning captain Hugo Lloris and the Belgian Vertonghen, who made the breakthrough on eight minutes.
Christian Eriksen's back post corner was met by Davinson Sanchez, whose header was knocked down into the path of Vertonghen. The Belgian headed goalwards and the ball richoted in off the underside of the crossbar, with goal line technology later confirming that it had crossed the line by all of nine milimetres.
Spurs were ahead for less than three minutes before Matt Ritchie's devilish ball was glanced home by Joselu, preferred to new signing Salomon Rondon as the spearhead of the Newcastle attack.
Within ten minutes Tottenham were back in front though, with Alli stealing in round the back post to head Serge Aurier's excellent delivery back across Martin Dubravka and in to the far corner.
Newcastle came close to levelling on several occasions in the second half, with Mo Diame rattling the outisde of the post with a half volley from the angle.
At the other end, Dubravaka made a superb reflex save to stop Moussa Sissoko from scoring against his former club.
As the second half wore on, Spurs' lack of match fitness began to show. While Alli continued to terrorise DeAndre Yedlin, Kane and England teammate Eric Dier both struggled as Newcastle seized the initiative.
Rafa Benitez brought on his new number nine, Rondon, and the Venezuelan nearly got his Newcastle career off to the dream start, only to see his 85th minute strike deflected onto the bar by Vertonghen.
