Bouchard, the 18th seed, was all over the Kerber serve from the outset and the left-handed German was caught cold. She was 5-0 down before she could draw breath in the face of the Canadian's accuracy, movement and variety of shot.
The first set went by in just 23 minutes but Kerber's serve was still her weak point and she was broken in the third game of the second set and again in the fifth.
Kerber ended her disappointing display by hitting a Bouchard second serve long on match point.
"I just felt good out there," Bouchard said. "I think I executed my game plan really well, so I'm happy with that. I was really mentally prepared for anything, for a battle.
"I'm confident and I really believe in my skills. I believe I can play with the best girls out there."
Bouchard reached the semi-finals at this year's Australian Open, when she lost to eventual champion Li Na, and won her first WTA title shortly before the French Open began.
"I feel like since the beginning of the year I have been improving my game, since Australia I'm at a different level from there," Bouchard said.
Kerber managed to win just 28 percent of points on her second serve, but Bouchard's all-round game was also far superior.
A stooping forehand down the line won Bouchard the first set after 23 minutes in front of a three-quarters empty Philippe Chatrier showcourt.
Kerber held her first service game of the second set, but hit long to lose her second, and wasted her one break point in Bouchard's following service game, when the Canadian smacked a backhand into the corner to reach deuce.
Two double faults and a couple of errors meant Kerber's third service game of the set also went in Bouchard's favour and the match was over after just 52 minutes.
The result was a turnround from their only previous meeting, at last year's U.S. Open, when Kerber won in three sets.
"I can say that it was not my best day today," said Kerber. "I was trying, but I had no rhythm. I made so many mistakes, I was not moving very good."
Last year's runner-up Maria Sharapova, the seventh seed, survived a shaky start to beat Australian Sam Stosur 3-6 6-4 6-0, winning the last nine games to set up a quarter-final against Spanish sensation Garbine Muguruza, who rounded off a bad day for the host nation with a 6-4 6-2 win against France's Pauline Parmentier.
Another fast-rising talent, Canadian Eugenie Bouchard thrashed German eighth seed Angelique Kerber 6-1 6-2 to claim a quarter-final spot, crunching 30 winners in 52 dazzling minutes to stretch her winning run on clay to nine matches.
Carla Suarez Navarro was a step too high for up and coming Croatian Ajla Tomljanovic as the Spanish 14th seed advanced into the French Open quarter-finals with a 6-3 6-3 win on Sunday.
Suarez Navarro used her one-handed backhand to subdue the unseeded Tomljanovic, who had knocked out third seed Agnieszka Radwanska in the previous round.
The Spaniard, who had reached the last eight at Roland Garros in her first appearance in 2008, prevailed on her second match point when Tomljanovic netted a forehand.
She will next face Canadian Eugenie Bouchard, the 18th seed.
Results from the French Open Women's Singles Round 4 matches on Sunday
Garbine Muguruza Blanco (Spain) beat Pauline Parmentier (France) 6-4 6-2
7-Maria Sharapova (Russia) beat 19-Samantha Stosur (Australia) 3-6 6-4 6-0
14-Carla Suarez Navarro (Spain) beat Ajla Tomljanovic (Croatia) 6-3 6-3
18-Eugenie Bouchard (Canada) beat 8-Angelique Kerber (Germany) 6-1 6-2
- Sports & Recreation
- Angelique Kerber
- Ajla Tomljanovic
- Carla Suarez Navarro