The England international, who joined the Citizens from Everton for around £50m last year, netted twice and helped keep the opposition at bay as his side ran out 4-0 winners at De Kuip on Wednesday night.
Stones struggled for consistency at times during his maiden campaign at the Etihad Stadium, starting 23 Premier League games in all, but Guardiola insists that the 23-year-old's defensive ability has never been in question.
"There is no doubt about his quality. His two goals were so important," he told reporters. "John knows what is the gap and where he has to improve, defending the duels, but he's so young and he is able to achieve. When he does, he will become an exceptional central defender."
Stones has now featured five times for City in all competitions this campaign, helping his side to three clean sheets.