After the completion of the Super League stage of the tournament, the top sic teams form the stage got the promotion to the Knock out level of the Ranji Trophy, 1998-99. The teams included the likes of Hyderabad, Delhi, Punjab, Tamil Nadu, Madhya Pradesh and Karnataka and the teams played against each other in the knock out matches of the Ranji Trophy, 1998-99 like the Quarter-Finals, Semi-Finals and Final. The teams fought with each other very hard for clinching the coveted championship title. However, though all the teams tried their best to do so, it was the Karnataka team that eventually won the championship title by beating the Madhya Pradesh team in the Final.

The first Quarter-Final match of the Ranji Trophy, 1998-99 was played between the teams of Hyderabad and Delhi and the two teams played the match at Secunderabad from 30 March-03 April, 1999. The Hyderabad team played extremely well in the match and thrashed the Delhi team with a huge margin of 438 runs in the match for getting into the Semi-Final stage of the tournament. The teams of Punjab and Tamil Nadu played against each other in the second Quarter-Final match of the Ranji Trophy, 1998-99 and the match was held at Amritsar from 30 March-03 April, 1999. The match remained drawn during the specified period of time and the match officials decided to allow the Punjab team to advance to the Semi-Finals, as it had a lead in the first innings of the match.

The Hyderabad and Madhya Pradesh teams played against each other in the first Semi-Final match of the Ranji Trophy, 1998-99 and the match took place at Secunderabad from 09-13 April, 1999. The drawn match saw the Madhya Pradesh team reaching the Final of the tournament for having a lead in the first innings of the match. The second Semi-Final match of the Ranji Trophy, 1998-99 was played between the teams of Punjab and Karnataka and the two teams played the match at Amritsar from 09-13 April, 1999. The Karnataka team played very well in the match for clinching a victory of 7 wickets and set up a clash with the Madhya Pradesh team in the Final of the tournament. Thus, the Madhya Pradesh and Karnataka teams played against each other in the Final match of the Ranji Trophy, 1998-99 and the two teams played the match at Bangalore from 19-23 April, 1999. Playing very well in the match, the Karnataka team clinched a victory of 96 runs for winning the match as well as the coveted championship title.