Pep Guardiola's men took a major step closer to becoming the first side to retain the title since United in 2009 with a comfortable 2-0 win at Old Trafford.
However, the England defender says they will not take the Clarets lightly as they battle Liverpool for the Premier League title.
"They're always a very well-organised team," Stones told Sky Sports, who has never previously played at Turf Moor during his playing career. "Taking nothing away from them, they've got quality as well.
"They've brought in some new players and have changed their style, and Joe [Hart] is there who we know well. It's never an easy game - they sometimes grind out results against the top teams so we know what we're up against.
"It'll be a very physical game and one that in previous seasons we've had to grab hold of early doors to set the tempo. We know that we're in for a game."