Sabalenka looked to be cruising after winning the first set and going a double break up in the next, only to spectacularly collapse and crash out.
The wind played a factor in her demise, as it did in the 2025 final, where the Belarussian lost to Coco Gauff.
The win for Shnaider means that in both the men's and women's singles draws, there will be a new Grand Slam champion.
Conditions on Court Philippe Chatrier proved a big challenge for both players as they affected precise shot-making, but Sabalenka found her groove for a 5-1 advantage in the first set before she dropped serve when the wind began to really swirl.
The Belarusian let out a frustrated scream after netting a backhand to give Shnaider another break point, but she composed herself again to wrap up the first set in 49 minutes and punch the air to loud applause from the crowd.
Russian 25th seed Shnaider dropped her level in the second set to fall behind again before mounting a spirited comeback to erase the double break and level at 5-5, before dragging four-times major champion Sabalenka to a decider.
Left-hander Shnaider's forehand caused all kinds of issues early in the final set for Sabalenka, and the 22-year-old broke for a 2-0 lead with a cross-court winner before holding firm to seal the win and set up a clash with Maja Chwalinska.
More to follow.
