The defender's 39th minute strike pushed City into a deserved top-six place, leap-frogging their lack-lustre opponents.
Having recently put a quartet of disappointing defeats behind them with a three-goal reverse of high-flying Burnley, the Baggies' promotion push was very much still on.
But Stoke, boasting an impressive home record, were to offer an acid test to Albion's resolve - and the visitors were fortunate not to be trailing after just 15 minutes.
Darel Russell, enjoying a rich run in front of goal, had a goal-bound drive charged down by Chris Perry before Mamady Sidibe's goal celebrations were nipped in the bud.
Vincent Pericard's enthusiasm to shake his escort triggered the linesman's offside flag before Sidibe had steered the loose ball into the vacant net.
Kevin Phillips went close to breaking a cagey deadlock after getting on the end of Jonathan Greening's centre, but it was the in-form hosts that took a deserved lead into the interval.
Russell turned on the turbo and burst into the danger-zone drawing the attention of three Baggies defenders before eventually being bundled over by Martin Albrechtsen.
Higginbotham duly fired in the resulting penalty with gusto to maintain his 100 per cent record as City's spot-kick specialist and then reeled away in celebration of his fourth goal this term.
The Potters' full throttle second-half approach had the travelling back-line in tatters and the hosts should have doubled their lead early on.
Russell looked destined to add to his three goals in his last five appearances, but drove wide after a rare glimpse of quality from Pericard had navigated a way through.
The 67th minute introduction of on-loan Premiership star Patrik Berger drew the afternoon's biggest ovation but a substitution five minutes prior almost made the biggest impact.
Zoltan Gera evaded the City radar and got onto a deep left-flank centre before directing a weak header into the grateful arms of Steve Simonsen.
Stoke's midfield was now brimming with a glut of on-loan Premiership class and the hosts' approach play was proving a mouth-watering spectacle.
Lee Hendrie and Sidibe both spurned late chances to finish it off after some real champagne football from Salif Diao and Berger respectively, had picked the visitors apart at the seams.