Although it was goalless at the break, the Villagers responded to four defeats in-a-row by taking the game to the hosts.
Thompson shot just wide from Taron Hare's cross, and Danny Clarke forced Sam Johnson into a good save.
It was no surprise when Thompson gave North Ferriby the advantage in the 49th minute. The deadline-day signing marked his first goal for the Grange Lane club by rounding the goalkeeper and slotting in from a tight angle.
Gus Mafuta's late strike almost levelled the scores, but North Ferriby held on for the win.
Report supplied by the Press Association.
Match ends, Gateshead 0, North Ferriby United 1.
Second Half ends, Gateshead 0, North Ferriby United 1.
Connor Oliver (North Ferriby United) is shown the yellow card for a bad foul.
Substitution, North Ferriby United. Ryan Fallowfield replaces Connor Robinson.
Mitch Brundle (Gateshead) is shown the yellow card.
Substitution, Gateshead. Adam Wrightson replaces James Bolton.
Substitution, North Ferriby United. Ryan Kendall replaces Reece Thompson.
Substitution, North Ferriby United. Danny Emerton replaces Jake Skelton.
Goal!  Gateshead 0, North Ferriby United 1. Reece Thompson (North Ferriby United).
Substitution, Gateshead. Gus Mafuta replaces Rhys Oates.
Substitution, Gateshead. Danny Johnson replaces Sam Jones.
Second Half begins Gateshead 0, North Ferriby United 0.
First Half ends, Gateshead 0, North Ferriby United 0.
Patrick McLaughlin (Gateshead) is shown the yellow card for a bad foul.
Sam Jones (Gateshead) is shown the yellow card for a bad foul.
First Half begins.
Lineups are announced and players are warming up.

Syria's 1-0 victory on Thursday shocked fans in the Chinese city of Xi'an who took to the streets.
China has said it wants to become a "world football superpower".
But the loss means the team could now miss out on a place in the 2018 World Cup in Russia.
China is ranked 78th in the world whereas Syria is 114th, just ahead of North Korea. The Chinese team faces Uzbekistan on 11 October which will decide if they qualify.
Tencent's sports website said large group of fans gathered on the streets outside the Zhuque stadium, demanding the resignation of Cai Zhenhua, president of the Chinese Football Association after the game.
"Resign, resign, resign!", they are heard shouting in a video posted to Twitter.
Online, fans were equally critical of the Chinese team's performance.
"The Syrian football team has proved that we aren't strong and victorious," said one user on micro-blogging site Weibo.
"I'm going to hide my face now," said another.
"My blood pressure literally rose when I was watching the game," a user said.
"Syria, a war-torn country who can't even afford to buy their own shoes or shirts, whose manager earns a monthly salary of 2000 yuan, defeated China whose players earn millions," one person said.
Syria, who play their home matches in Oman due to the war, has seen almost five years of armed conflict.
Earlier this year, China laid out an ambitious plan to become a "world football superpower" by 2050.
The country's President Xi Jinping, a football enthusiast, previously said he wanted China to win the World Cup in 15 years.
The country also wants 50 million children and adults playing the game by 2020.
"The president of the country is pushing for football," Sven-Goran Eriksson, who coaches the Chinese Super League, told the BBC earlier this year.
"He wants China as a national team to be big, to be better in football."
Reece Thompson's second-half goal handed North Ferriby their first ever away win in the fifth tier as they beat struggling Gateshead.
[NEXT_CONCEPT]
Angry Chinese fans have called for the resignation of the president of China's football association, after the country lost to Syria in a World Cup qualifier.