After a lacklustre opening 45 minutes in the Midlands, the game was settled by the Spaniard???s strike after 63 minutes ??? his third goal since signing for the Potters.
His one-touch to control with his right before swivelling and finishing with his left was the game’s real moment of quality.
Leicester had the better of the chances in an uneventful first period but efforts from Anthony Knockaert and Jamie Vardy drew Stoke keeper Asmir Begovic into comfortable saves and never really threatened to open the scoring.
New Stoke defender Philipp Wollschied squandered a decent chance to break the deadlock for the visitors but it was Bojan who ultimately settled the contest.
After going a goal behind, Nigel Pearson introduced Leicester???s new signing Andrej Kramaric into the fray but his involvement, along with that of substitutes Leonardo Ulloa and Tom Lawrence, did little to alter proceedings.
The result sees the Foxes surrender their four-game unbeaten run in all competitions and remain rooted to the foot of the table, while Stoke leapfrog Newcastle, momentarily, into the top half of the table.
Stoke captain Ryan Shawcross was forced to miss the game after he failed a late fitness test before kick-off. But, to the visitors??? credit, Leicester didn???t take advantage of his absence as it was the away side who started the game stronger, controlling almost 90 per cent of the ball in the opening five minutes of the game.
Potters duo Bojan and Victor Moses, who returned to the first team for the first time in eight weeks, tried to initiate a number of attacks for the visitors but they came up against a resolute and well-drilled Leicester back four.
The Foxes took a while to get going but the game???s first chance fell to the hosts just before the half-hour mark.
After Paul Konchesky and Andy King had found each other just inside the Stoke half, the midfielder found Jeff Schlupp down the left channel. The Ghana international picked out Anthony Knockaert, who was late entering the area, but the Frenchman???s resulting shot was straight at Begovic which allowed him to collect with relative ease.
The chance appeared to buoy Leicester and David Nugent tried his luck from a similar position to which he struck the bar against Aston Villa last weekend. This time, after collecting Vardy???s pass, Nugent opted to curl a shot toward the far corner of the Stoke goal, a decision which would have paid off had the shot been a yard lower.
Stoke then had a great chance to open the scoring when Wollschied rose highest to meet Moses??? corner on 37 minutes. The German appeared to do everything other than connect well with the ball and fired a tame effort wide of the target, although Drinkwater was on the post to prevent it going in.
Leicester had the last chance of the first half. Schlupp was involved again, collecting Drinkwater???s pass before finding his strike partner Jamie Vardy who escaped the clutches of Wollschied before producing an eye-catching back-heeled flick towards goal which Begovic collected comfortably.
Stoke started the second half in similar fashion to which they had the first and created the first opportunity as Moses tormented several Leicester defenders before threading an inch-perfect pass into the path of Marco Arnautovic.
The Austrian collect the ball in the right-hand channel of the box and, instead of shooting across goal, opted for a near-post finish which nestled into the side netting.
Neither side seemed able to dominate the game until Bojan intervened just after the hour mark. Walters collected the ball on the right wing, fed it into the former Barcelona player???s feet and watched as he first stopped the ball with one foot and finished with the other inside Hamer’s left-hand corner.
Leicester were stunned and tried to push for an equaliser but never came closer than Knockaert???s deflected effort in the closing stages.