didn’t get along with him and drove him away. This article does a good job of summarizing what happened:

“Jimmy Johnson and Jerry Jones mutually agreed to split due largely to their growing inability to work together. Johnson's relationship with Jones began to fall apart in 1993. It started with Jones wanting more say in player personnel decisions. Although Jones had the title of general manager, Johnson had the final say in football matters and was unwilling to give it up. In March 1994, after the Cowboys had won their second Super Bowl under Johnson, Jones angered Johnson when he told reporters that any coach could have led the Cowboys to a Super Bowl. Another incident happened in December 1993...Johnson had said he was interested in becoming head coach of the expansion Jacksonville Jaguars. This led to Jones telling the media that he alone would decide Johnson's coaching future. They agreed to part ways on March 28, 1994, after the Cowboys had won their second straight Super Bowl, with Johnson getting a $2 million bonus.”