With top seed and defending champion Williams also having brushed past French qualifier Marion Bartoli 6-1 6-2, Thursday's semi-final will provide both players with their first big test in the $2.96 million hardcourt tournament.
Dokic, the ninth seed from Yugoslavia, could do nothing to counter the Belgian's power and third seed Clijsters needed just 53 minutes to wrap up her fourth victory in five days.
Clijsters, who has not conceded more than two games in any of the eight sets she has played, told reporters: "These are the matches, when you're younger, when you're practising, that you dream of."
"I love playing these big matches. I just hope I'll get more than two games against her," she joked.
In 2002, Clijsters was the only player to beat both Serena and Venus Williams, outplaying Serena in the final of the season-ending WTA Championships in Los Angeles.
Serena, however, won their most recent meeting. In the semi-final of the Australian Open in January, she retrieved a 5-1 final-set deficit and went on to become only the fifth woman to hold all four grand slam titles at the same time.
"I don't think I did anything wrong in that match, she just raised her level," Clijsters said.
"Against Jelena, you have to be there for every point and show you're fighting because once she gets ahead, she can really dominate and overpower you."
Dokic conceded she had been outplayed. "I hit the ball very well for the first half-hour but she got everything back so I don't feel I played too badly," said the Yugoslav.
"She played so well and didn't make any errors so I can't beat myself up too much."
Venus, the second seed and three times champion, fell in straight sets to Meghann Shaughnessy on Monday.
Bartoli, 18, benefited from the withdrawals through injury of Monica Seles and Lindsay Davenport on her way to the last eight and produced a gutsy display on the Stadium Court that belied the scoreline.
She broke Serena's serve three times and provided the top seed with some exercise along the baseline with several testing service returns.
Bartoli was let down, though, by her poor second serve, with which she won just four of 26 points.
Williams said that her sister's defeat, her first in this tournament by anyone other than Serena since 1997, made her more determined against Bartoli, who is a career-high 87th in the world.
"I definitely figured it would be a tough match. I've seen her play before and she's a tough cookie," said the world number one. "She never gives up and has a lot of determination in her eyes."
Bartoli plays all her shots, forehand and backhand, with both hands on the racket. She said she was so excited about playing Williams that she was up at 7am trying to drag her father Walter, who is also her coach, to the stadium.
"I enjoyed the moment because it's such good experience and I'm not going to play against her every day," said Bartoli, who as a qualifier in last year's US Open upset Arantxa Sanchez Vicario on her way to the third round.
"But my goal is to be a top 10 player, to play more times against her and to beat her one time, so I am not going to say 'Oh, it was just a great experience'."
In the other half of the draw, Justine Henin-Hardenne of Belgium, the third seed, will play Chanda Rubin, the American world number 10, on Wednesday. The other quarter-final is an all-American affair between Shaughnessy and Jennifer Capriati.
