They went ahead in contentious circumstances, Callum Wilson finding the net with an excellent lob from outside the box after colliding with Hugo Lloris.
The goal was awarded after a lengthy video assistant referee (VAR) check for a foul and handball, but there was nothing controversial about the second goal before half-time.
A poor clearance by Lloris was intercepted by Sean Longstaff before Miguel Almiron beat one opponent and went around another and fired under the Spurs keeper for his fifth goal in five league games.
Spurs pulled a goal back through Harry Kane’s low header from close range, awarded after another lengthy VAR check for offside, but Newcastle held on to secure the points.
While the Magpies extended their unbeaten league run to seven games, Tottenham have now lost their last two and are in danger of going backwards.
They started positively with Son Heung-min and Harry Kane both denied by visiting keeper Nick Pope.
But, with thunder and lightning in the air, Spurs struggled to carve out chances as the weather deteriorated and in the end they could have few complaints about the outcome.
Meanwhile, Newcastle’s players and staff celebrated on the pitch in front of their jubilant travelling fans.
Newcastle crumbled to a 5-1 defeat at Spurs six months ago but they are a different proposition this season and their campaign goes from strength to strength.
They have not played in Europe since 2012-13, while not since 2002-03 have they appeared in the group stage of the Champions League.
But manager Eddie Howe and his players have their fans dreaming of a return to the continent after another efficient performance.
Once again Newcastle were well organised and continue to pick up points despite missing forward and record signing Alexander Isak, who has been out since September with a thigh injury.
Even after Kane gave Spurs hope with his 10th league goal of the season, the Magpies did not panic, with Fabian Schar and Sven Botman frustrating the hosts when they piled forward in search of an equaliser.
Newcastle are establishing a reputation for being hard to beat. Their last defeat was on 31 August at Liverpool when they conceded a 98th-minute goal.
There is a long way to go and bigger tests to come but Newcastle look good value for their place in the top four. Tottenham remain third in the table but boss Antonio Conte will be a worried man after a second defeat inside a week.
Wednesday’s 2-0 setback at Manchester United was a missed opportunity to show what a force they could become under the Italian.
On Sunday, they started on the front foot before fading as their impressive 10-match winning run at the Tottenham Hotspur Stadium came to a grinding halt after an underwhelming performance.
There will be complaints from the home dressing room that Newcastle’s first goal was allowed to stand with Rodrigo Bentancur booked for arguing with the referee about the decision.
But even after Kane reduced the deficit, Spurs did not test Pope enough as they lost at home for the first time since 16 April.
The games are coming thick and fast and Conte will demand an improved performance against Sporting Lisbon in the Champions League on Wednesday.