The 15th-seeded Frenchwoman led 3-0 in both sets and took 62 minutes to wrap them up. Flipkens, a Belgian seeded 20th, was in her first major semifinal.
"I was hitting the ball very cleanly from the start, right away," Bartoli said. "I had some great passing shots and some great lobs. Everything was working so perfectly. To do that in the semifinals of Wimbledon was an amazing feeling."
Bartoli also reached the final in 2007, losing to Venus Williams in straight sets. She next faces the winner of Thursday's other semifinal between fourth-seeded Agnieszka Radwanska of Poland and No. 23 Sabine Lisicki of Germany. Lisicki eliminated defending champion Serena Williams in the fourth round.
None of the four semifinalists has won a Grand Slam title.
Amelie Mauresmo, the 2006 Wimbledon champion who coaches France's Fed Cup team, was in the stands for the early match and had plenty of praise for Bartoli.
"She just played a great match, definitely the best match of the tournament for her," Mauresmo said. "Marion put huge pressure on her right from the beginning, first of all returning very well, serving better, which she had to do today."
Bartoli was pumped from the start on Centre Court, mixing two-handed backhands and forehands with little hops between points, as she usually does.
In the first set, she faced only one break point, nearly putting Flipkens back on serve in the third game. But despite a double-fault and a backhand into the net to eventually get behind 30-40, Bartoli dug herself out of the hole and finished the game with the first of her five aces.
Flipkens, who again took the court with her right knee taped, called for a trainer after being broken for the second straight time at the start of the second set. The trainer added tape to the knee while Bartoli sat in her chair sipping water.
Whatever she needed, it briefly worked. Flipkens, after the medical timeout, broke for the first and only time, making it 3-1. But a few minutes later Bartoli broke again and held to make it 5-1.
"I think maybe she was a bit injured today," Bartoli said. "It must be hard for her to be injured in the semifinal of Wimbledon, but she deserved a lot of respect."
Bartoli is now 2-1 in Grand Slam semifinals with both wins at Wimbledon. Six years ago, she beat another Belgian, top-seeded Justine Henin, in the semifinals. But then she ran into Venus Williams, who that year won the fourth of her five Wimbledon titles.
On Saturday, Bartoli will be on relatively equal footing against another player -- Radwanska or Lisicki -- looking for a maiden major title.
"It's a good opportunity. She has experience at least," Mauresmo said, referring to Bartoli. "Maybe it's going to help her for the final."