Stones, 23, has not featured for the Premier League champions since the beginning of March after he picked up an abductor injury on international duty.
There had been rumours the centre-back, who signed a six-year contract when he joined from Everton in August 2016, could be a surprise departure in the next transfer window.
Guardiola, however, was definitive when asked to respond to reports Stones could be among those on their way out of the Etihad Stadium.
“I don’t know how people believe we’re going to sell John Stones,” Guardiola said.
“He is a young player, an international English player. He’s a huge part of the reason why we won the title.
“I don’t know how long I will be here in Manchester, but as long as I’m here, John Stones will be with us.
“When he is injured and comes back, injured and comes back, injured and comes back, sometimes it’s not easy.
“I’m sorry for the guys who announce we’re going to want to sell him. I’m sorry – they lie. I’m not going to comment on the transfers when it’s fake news.”
Guardiola has favoured Vincent Kompany and Nicolas Otamendi at the heart of City’s centre and the pair are expected to continue for Sunday’s fixture against West Ham at the London Stadium.
However, Stones may get the opportunity to feature in City’s final three matches against Huddersfield, Brighton and Southampton with Guardiola satisfied with the attitude of the defender.
“First of all, he (Stones) is an amazing guy and he’s going to stay here with me,” he said.
“He is a joy to train, I want to help him, and we cannot forget the first six months with Nicolas Otamendi was excellent, was top.
“Vinnie (Kompany) came back at a good level, Nico has been at an amazing level all the season, and Aymeric Laporte – his impact from the beginning was so good. All four know they have to compete between them.”
Guardiola, meanwhile, believes his side’s attacking approach this season has proved wrong those who previously doubted his purist principles could deliver silverware.
He famously said after a 4-2 defeat to Leicester in December 2016 that he “didn’t coach tackles” and believes that statement has been vindicated.
“Now it looks like we won I’m saying, ‘Ok, I was right in that situation’,” Guardiola said.
“Tackles are a part of the game. But there are many, many subjects about football and I’m not focused on tackles.
“Tackles are like a talent. Some are good in the headers, some shoot well, it’s an important part of the game.
“We were a team this season that conceded few goals and chances because we defend well and that’s because we win duels and tackles.”