Yost now has 543 wins with the Royals after getting 457 with the Brewers.
"When I started this, I just had two goals," Yost said. "One was to help a team win a world championship and the other was 1,000 wins. I thought 'If I'm good at this job, I'll be around long enough to get 1,000 wins.'
"It just kind of came because I had great players and great general managers in Doug Melvin and Dayton Moore."
Yost's victory total ranks seventh among active managers and tied him with Charlie Manuel for 61st on the all-time list. Yost managed the Brewers from 2003-2008 and took over the Royals' managing role on May 13, 2010.
"Ned's 1,000th win is a big deal," said right-hander Dillon Gee, who contributed to the victory with 4 1/3 innings of solid relief. "It's a good night all the way around."
Yost did an on-field interview in salute of his milestone before coming in for his usual postgame news conference.
He'll remember No. 1,000 as a night when the pitching was excellent, which was reminiscent of how the Royals battled their way to a world championship in 2015.
Jason Vargas, making his first appearance since Tommy John surgery 14 months ago, worked the opening three innings and allowed just one run. Then three relievers --- Gee, Joakim Soria and Wade Davis -- combined to hold Chicago to one run over the final six innings.
"The plan going in was to get three out of Vargy and four or five out of Dillon," Yost said. "We knew we would have to throw Joakim in there if Dillon could only go four. [Soria] came in and did a great job."
Robert Falkoff is a contributor to MLB.com based in Kansas City and covered the Royals on Saturday. This story was not subject to the approval of Major League Baseball or its clubs.