The 58-year-old Scot became Britain's most prolific trainer when veteran Italian jockey Frankie Dettori rode 20-1 shot Poet's Society to victory in the Clipper Logistics Handicap race at York in northeast England.
Johnston passed the mark of Richard Hannon Sr., who retired after 43 years as a trainer in 2013.
"It feels a relief to get it out of the way," Johnston told BBC Sport. "Sometimes you wonder how important it is. I have got to pinch myself to think we got to 4,194. From where we started it is unthinkable."
Dettori told reporters Johnston's achievement was "remarkable," praising the handler's great "consistency of training 200 winners year in, year out."
"He's a very nice fella to ride for, and because of this winner my picture is going to be in the downstairs loo forever in the Johnston household," Dettori said.
Johnston, a former veterinarian, borrowed money from his in laws and took out a mortgage to buy his first stable in Lincolnshire, England in 1987. His first win came the same year with Hinari Video at a racecourse in Cumbria, north west England.
His motto "Always trying" is emblazoned on the side of his horseboxes, and he has emulated Hannon's approach to racing his horses more often than some other trainers.
"[Hannon] was also a great believer in running his horses," Johnston said.
"He had a big team and ran them a lot. Some people would have tried to belittle the numbers and said they were not as important as the quality, but to my mind you've got to do both.
"Certainly, if I was an owner, I wouldn't want my horse in a yard where the chances of it never running, never mind winning, were fairly high, and that does apply to a lot of yards."
Johnston's career has been full of quality horses, including two British Classic wins and three Ascot Gold Cup triumphs.
He rates Attraction, who won the 1,000 Guineas in both England and Ireland in 2004, as the one he is most proud of.
"There were so many down times in her career, to win five Group 1s with the injuries she had - injuries that would have ended other horses - nothing was going to end her career," he said recently.
However, Johnston reserves the most praise for Sharmadal, who was the champion two-year-old in Europe in 2004.
"I never thought I'd have another one as good as Attraction but then I had Shamardal for one season and three starts. Four Group 1 wins, he's the best I have ever had," he added.