It was the 29th meeting between the Williams sisters - Serena now leads 17-12 - and it lasted 87 minutes in front of a main stadium crowd of more than 10,000 fans, including current world number one Simona Halep.
Venus had won just 1 of the pair's last 9 matches, making this 3rd round match 2nd in 10th.
She missed a handful of basic shots in the first set and couldn't get her serve going the way she typically did in the past.
Serena regained one of those lost breaks, but soon gave away another break of her own, which meant her second break at 2-5 did not prevent Venus from having an opportunity to serve out the match, which she duly took. However, Venus held on to her advantage and beat her sister in two straight sets for the first time since the 2008 Wimbledon final.
Venus is now positioned to be the top contender to win this week at Indian Wells Tennis Garden in California. And there was prevalent rust, even in her two wins. But from then on Venus made fewer mistakes and took a commanding lead. "She was asking what she was doing wrong, and I was trying to tell her she was rushing too much", Mouratoglou said.
Elsewhere, Australian Open champ Caroline Wozniacki benefited from a challenge call in the final game en route to defeating Aliaksandra Sasnovich 6-4, 2-6, 6-3. Serena came back in 2015 only to withdraw with a knee injury before her semifinal, and Venus followed the next year.
"That's, you know, totally gone out of my mind", she said. They sat with their backs to each other, with Serena on the back of the cart with Beats headphones over her ears. "So I have just got to keep saying each tournament my goal is just to be better than the last", Serena said. "I want to continue to go forward". It's definitely not less disappointing. Even with the baby, like, a trial run of traveling with the baby and all of this is just so new to me. She got off to an bad start in 2018, losing in the Round of 128 in the Australian Open, but she's a high-ranked, terrific player.