The 19-year-old midfielder appeared to break his leg after a red-card challenge from Ryan Shawcross that had echoes of team-mate Eduardo's own bad injury two years ago.
Stoke had led early on from a Danny Pugh goal but Nicklas Bendtner levelled before Cesc Fabregas struck a last-minute penalty and Thomas Vermaelen added another in injury time.
Arsenal's win lifted them to within three points of leaders Chelsea and ended Stoke's 11-match unbeaten run, but it is Ramsey's injury that will grab the headlines.
Shawcross appeared to be in tears when he left the field and a number of other players were clearly upset by the incident.
Arsenal had begun the game by handing veteran Sol Campbell his first Premier League start since rejoining the club last month.
Partnering Vermaelen, the former England defender was expected to have plenty of Rory Delap throws - a recent Arsenal weakness - to deal with and it was not long before they were tested.
Having been undone by the Irishman's potent weapon on their previous two visits, the trepidation amongst the back line was obvious as Delap lined up his first throw after four minutes.
It was probably much to their relief that Mamady Sidibe headed wide from a long throw close to Tony Pulis' technical area, but they were to be examined again soon enough.
That Arsenal had not learned from previous experience was clear as Alex Song's natural instinct to put the ball out for a throw rather than concede a corner kicked in.
That allowed Delap to launch another missile from level with the six-yard box.
Delap picked out Shawcross with a flat delivery and the defender's glancing header allowed the onrushing Pugh, just onside, to nod in at the far post.
Delap continued to bombard the Arsenal penalty area at every opportunity, from right and left, but the Londoners managed to clear the next three throws, albeit uncomfortably, without further damage.
It took 25 minutes for Arsenal to muster an effort on goal, Fabregas controlling a bouncing ball yards out and forcing Thomas Sorensen to concede a corner.
That allowed Arsenal to settle and they finally began to win some possession in a congested midfield.
They equalised after 32 minutes with a clever throw-in routine of their own.
Bacary Sagna went short to allow Fabregas to cross from the right and his pinpoint delivery was met by a looping header across goal from Bendtner 10 yards out.
Arsenal controlled the rest of the first half but had only one serious opportunity when Fabregas fired a free-kick into the wall.
The visitors appealed for a penalty early in the second half as Ramsey was met, after twisting into the box, by a clumsy challenge from Abdoulaye Faye but referee Peter Walton gave nothing.
The ball found its way out to Gael Clichy but the left-back's low shot was straight at Sorensen.
Delap troubled Arsenal again with another throw but Walton spotted an infringement in the area.
Emmanuel Eboue went close to giving Arsenal the lead with a fierce drive from outside the area just after the hour but Sorensen tipped over.
That proved the last meaningful action before the incident that completely changed the complexion of the game.
Play was held up for five minutes after Ramsey's leg buckled under contact from Shawcross, who had taken a heavy touch and stretched for the ball.
Other players showed immediate concern and waved for immediate attention.
Arsenal did well to summon some fighting spirit after Ramsey's loss with Tomas Rosicky firing wide when well placed.
Substitute Eduardo, just over two years after his own injury nightmare, then spurned an even greater opportunity when he broke into the area and shot into the side-netting.
Persistence paid off and Arsenal were given the chance to snatch victory when Bendtner's flick into the area was handled by Pugh.
Fabregas stepped up to squeeze a low spot-kick into the bottom corner and spark emotional celebrations.
Arsenal added a third during seven minutes of injury time as Sorensen parried a Rosicky shot and Eduardo squared for Vermaelen.
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