Stones became the world's second most expensive defender when he joined City for an initial £47.5 million from Everton last August.
Impressive early season showings gave way to some error-stained displays alongside Nicolas Otamendi and converted left-back Aleksandar Kolarov at the heart of defence.
Club captain Kompany has been restricted to five senior starts this term as he attempts to put a succession of persistent fitness problems behind him and was ruled out of Saturday's 0-0 draw at Huddersfield Town in the fifth round of the FA Cup.
Stones played 90 minutes as Pep Guardiola's improving defence kept a fourth clean sheet in five matches but Ferdinand feels the 22-year-old has suffered without Kompany's steadying presence.
"Stones has clearly been asked to go out there and take risks, and I admire that," Ferdinand said, as quoted by ESPN. "I'd like to have played under Guardiola because I would have enjoyed going out there and taking the ball.
"But it's about balance and getting that right. What the manager is asking particular players to do is the difference and that's why Stones needs a Vincent Kompany next to him because the centre-halves he is playing with are not experienced enough in this country.
"He hasn't set the world alight, nor has Nicolas Otamendi, but if Kompany had been fit enough to play alongside him, it would have helped him and guided him because he is still a young player coming into a new team."
Parallels have been drawn between Ferdinand and Stones – both gifted, ball-playing defenders who attracted early career criticism for playing their way into tricky situations.
Ferdinand smoothed out the rough edges of his game at United to become one of the world's premier centre-backs but he wonders whether Guardiola's expansive style at City will allow Stones to make similar adjustments.
"When you go to a big club for big money, it isn't easy," he said, having become the most expensive footballer in Britain when he moved from Leeds United to Old Trafford in 2002.
"At United, I went into a team where everyone knew their roles, but it was still a challenge for me. The problem is that I went there thinking about how many skills I could do on a pitch rather than clean sheets.
"I think Stones is still having more concerns about the football side of the game rather than defensively. They have more of the ball than teams they play against too, so there is a lot of information to take in if you are a Pep Guardiola centre-half - things like splitting to get the ball and then, 'What is the next phase after that?'
"At United, I toned my game down rather than being on the front foot. It was more about my first thought being 'clean sheet, where are we defensively, concentration, etc.,' then the football stuff came naturally.
"But I think Pep asks more of his centre-halves on the ball than in the teams I played in, so it is a big ask and it is harder because of that. My position when I didn't have the ball was to be in a position to stop the counterattack, whereas it seems Pep Guardiola says and wants differently."