The winger struck four minutes from time to send the 2,100 Seasiders absolutely delirious at the bet365 Stadium.
The Seasiders had largely dominated from the first minute, but were guilty of squandering some gilt-edged opportunities.
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Thankfully they weren’t made to pay for those misses by a passive, out-of-form Stoke side, who left in their droves as Bowler won it at the death.
The victory, Blackpool’s second in a row, was their first on the road since the 1-0 win at Sheffield United four months ago.
It was a great way to mark Neil Critchley’s two-year anniversary, as the Seasiders four points ahead of the Potters.
With Jordan Gabriel now sidelined with a hamstring injury, Neil Critchley opted to move Dujon Sterling back over to his natural position of right-back.
Reece James, meanwhile, took Gabriel’s space in the side and slotted in at left-back.
Elsewhere, Shayne Lavery came in for Jerry Yates after scoring off the bench in last week’s 4-1 win against Reading, the second of Blackpool’s two changes.
Chris Maxwell (quad), Richard Keogh (calf), Luke Garbutt (knee), James Husband (hamstring), Matty Virtue (ACL), Grant Ward (achilles), Sonny Carey (metatarsal) and Keshi Anderson (hamstring) all remain sidelined.
Yates dropped down to the bench, where he was joined by the likes of Owen Dale, Charlie Kirk and Jake Beesley. Ethan Robson was left out of the squad altogether.
Stoke, who began the day one point below the Seasiders in the league table, made three changes from their midweek defeat to Crystal Palace in the FA Cup.
Before kick-off, both sets of supporters stood in solidarity with Ukraine with a minute’s of applause, while Blackpool fans added chants of “Putin is a w*nker”.
The Seasiders made a bright start to the game, getting on the ball nice and early and dominating the early possession.
On three minutes, the returning James swung in a teasing cross from the left which just evaded Gary Madine, who was at full stretch at the back post.
The Seasiders maintained their pressure, forcing Stoke into mistake after mistake thanks to their ferocious closing down.
Critchley’s side squandered two big chances in the space of 60 seconds, both involving CJ Hamilton.
Shayne Lavery got in behind Stoke’s backline for the first opportunity, squaring the ball to Gary Madine whose shot was blocked. The ball immediately fell to Hamilton but he was unable to get the ball under control.
The winger ought to have laid the ball on a plate for Madine a few seconds later when he had acres of space and all the time in the world to pick out the Blackpool striker, but he somehow managed to overhit his cross and the chance went to waste.
The Seasiders almost lived to regret those missed opportunities as Stoke went close to taking the lead completely against the run of play.
Josh Tymon swung in an inviting cross beyond Marvin Ekpiteta and Jordan Thorniley, but Nick Powell somehow managed to skew wide at the back post.
The frantic start to the game continued as Blackpool missed another gilt-edged chance to take the lead.
The chance came after the visitors forced Stoke into making yet another mistake, allowing Hamilton the space to roam forward.
Once again he failed to pick out a teammate, but the ball did end up ricocheting to Madine who showed composure to cut inside his man to open up space for himself 10 yards from goal, but Jack Bonham stood tall to thwart him.
Nevertheless, the Seasiders remained well on top thanks in part to their terrific off-the-ball work, which saw them cut down the angles at every opportunity to stop Stoke playing through the lines.
The chances continued to come, but Blackpool still weren’t able to find that final touch in front of goal.
To Josh Bowler’s credit, he did superbly to even create a chance for himself after linking up well with Madine before dancing his way through the Stoke backline. But again Bonham came to Stoke’s aid.
While the home side weren’t really at the races for much of the first-half, they still offered an attacking threat every now and then.
After Reece James was booked for a needless foul, Mario Vrancic swung in a dangerous ball which Powell headed wide at full stretch.
The hosts, still well and truly second best, came inches away from breaking the deadlock three minutes before the interval when Josh Maja hit the woodwork.
The former Sunderland striker wrong footed Dan Grimshaw with a low, scuffed effort from the edge of the box which - fortunately for Pool - struck the foot of the post.
Stoke offered a bit more at the start of the second-half, although it probably would have been impossible to get any worse. Needless to say, they still weren’t overly convincing.
The hosts did enjoy a spell of pressure midway through the second-half, but the Seasiders held firm and defended well thanks to some vital blocks and interceptions.
The second 45 minutes was largely a dull affair, summed up by Stoke substitute Tyrese Campbell volleying about 20 yards wide after a catalogue of errors from both sides led to the opportunity.
The game was temporarily halted with 15 minutes to go when Jordan Thorniley fell to the turf clutching his neck following a shove in the back from Josh Maja.
Pool, already without centre-backs James Husband and Richard Keogh through injury, were forced into a change as Ollie Casey came on in Thorniley’s place.
Jerry Yates, meanwhile, soon followed as he replaced Lavery for the final seven minutes, plus the lengthy stoppage time.
Just as the game looked to be fizzling out, the Seasiders broke the deadlock with just four minutes to go.
And guess what? Yates was instrumental as he held the ball up superbly before combining with Bowler, who lashed home to send the 2,100 Pool fans behind the goal absolutely wild.
It’s now six in eight games for Bowler, who has been in sensational form for the past two or three months.
Madine missed a glorious chance to make it two in the final minute of normal time, side footing over from Hamilton’s left-wing cross.
Due to the earlier stoppage, the Seasiders had to withstand eight minutes of stoppage time to see out their win.
Saying that, it could have been a different story as Steven Fletcher went through on goal in the dying seconds, only to be denied by a HUGE save from Grimshaw.