The £2.75million summer signing from Ipswich scored the winner in the 47th minute.
It was a special moment for Walters given that he played for Blackburn in his youth before joining Bolton.
The 27-year-old has been on a long journey but has settled in quickly in his new surroundings.
It was Stoke's second successive victory following the win over Newcastle and Blackburn could have little complaint.
They rarely looked an attacking force with Mame Diouf ploughing a lone furrow up front.
Not only that, Matthew Etherington and Jermaine Pennant were both busy down the flanks for the home side while Dean Whitehead put in a hard shift in the middle of the park.
Stoke got quickly into their stride and goalkeeper Thomas Sorensen released Etherington with a long throw. He raced down the left before delivering a cross into the area only for Brett Emerton to make the clearance with Jermaine Pennant lurking.
Stoke maintained the momentum and Kenwyne Jones made space for himself before sending a 20-yard shot wide of the post.
Blackburn again found themselves on the back foot in the eighth minute when Etherington picked out Jones but his header failed to test goalkeeper Paul Robinson.
This was a good spell by Stoke and a long throw from Rory Delap took a deflection and came back off the post in the 10th minute. Etherington latched on to the rebound only for Robinson to turn his effort over the bar.
Blackburn responded and almost took the lead in the 15th minute. Emerton's delicate chip beat Sorensen but Ryan Shawcross was on hand and averted the danger.
It was brief respite, however with Delap's long throw finding Jones. He got up high but his header was taken cleanly by Robinson.
Stoke kept up the pressure and Etherington found space on the left, only to see his well-struck effort go narrowly off-target.
Then Etherington was denied by Robinson in the 35th minute after Pennant delivered the cross.
Blackburn were being limited to counter-attacks and Phil Jones cracked in a shot from inside the penalty area three minutes later but it was blocked by Robert Huth.
Stoke made the breakthrough two minutes into the half after a towering leap from Jones released Etherington.
He threaded the ball through to Walters, who had timed his run to perfection before drilling a shot beyond Robinson.
Stoke almost added a second in the 53rd minute when Etherington's free-kick sailed over the wall but Robinson parried it to safety.
Blackburn boss Sam Allardyce decided to reorganise his team and brought on Martin Olsson for El-Hadji Diouf.
Olsson had settled quickly into the game and fired in a shot from an acute angle that Sorensen was happy to deflect for a corner.
However with time beginning to run out former Manchester City striker Benjani Mwaruwari was introduced by Blackburn with Emerton going off.
Stoke, though, came close to extending their lead in the 78th minute when Jones peeled away from his marker to get on the end of a cross from Etherington - only to head wide.
Then substitute Ricardo Fuller, who had recovered quickly after dislocating his shoulder at Newcastle, fired wide after a solo run.
Blackburn kept pushing men forward in the search for an equaliser but were unable to break Stoke down and build on their victory against Blackpool.