With the Potters holding Chelsea to a 1-1 draw following Jon Walters' penalty which had cancelled out Willian's early goal from a free kick, Conte opted to switch formation from his usual 3-4-3 to a 4-2-3-1 by replacing Victor Moses with Cesc Fabregas.
The move paid off as the Spaniard's corner kick was headed by David Luiz to Erik Pieters, who unwittingly sent the ball into the path of Gary Cahill - who had earlier given away a penalty.
The Chelsea defender smashed it into the back of the net to secure a 2-1 win, which sends the Blues temporarily 13 points clear of second-placed Tottenham.
Much of Chelsea's success this season has been built on Conte's 3-4-3 set-up, which he first tried out in the second half of the Blues' 3-0 loss to Arsenal before implementing it for the trip to Hull in early October.
But after changing his system again on Saturday, Conte admitted he wanted Chelsea to walk away from Stoke with all three points even though the Blues already boast a significant lead at the top of the Premier League standings.
When asked why he had changed his formation, Conte replied: "This is not the first time. This happened against Burnley.
"When you want to take more risks, to try to take three points and not only one, to try to change.
"For sure there is the great possiblity to score the goal, but also to concede a goal.
"You must know this but then I prefer to decide and risk to take three points. In other situations I decide to keep the result."