Kerber becomes only the fifth female No. 1 seed to lose in the opening round of a Grand Slam in the Open Era.
"For the first time in nine years at Roland Garros, I played my singles on (Court) Philippe Chatrier," Makarova said on-court after the one hour, 22-minute match. "She's a great player, I knew that she wasn't going to miss it, and that I had to win it."
Makarova, a two-time grand slam semifinalist, struck 26 winners in 16 games, served at 73 percent, and broke Kerber six times to improve to 5-1 against top 10 players this year.
"I think she played a good match. It was a tough first round," Kerber said after the loss. "I had a few chances in the first set and also in the second set, and I didn't make it. I think that was the key for the match. I believed in the second set, as well, that I can turn around the match and I was still believing until the last point, but she played well."
Kerber struggled with 25 unforced errors against just 16 winners, and won less than 50 percent of points behind her first serve. She was just two of 16 on break-point opportunities in the match, which included letting seven slip by in the final game.
With Kerber's stunning exit, the world No. 1 ranking can change hands after the French Open. No. 3 Karolina Pliskova of Czech Republic can move to No. 1 by reaching the final, while No. 4 Simona Halep of Romania can move to the top by winning the title. American Serena Williams, ranked No. 2, is sitting out the rest of the season due to her pregnancy.
This marked Kerber's 11th consecutive trip to the French Open with her best coming in 2012 when she reached the quarterfinals.
Last year Kerber won the Australian Open and U.S. Open, and was the Wimbledon runner-up, while this year has been much more of a struggle with a 19-13 record, losing four of her past six matches.
Kerber, who also lost in the first round of last year's tournament, now sees her clay-court season come to a close.
"Of course, I'm disappointed that the clay-court season was not so good," Kerber said. "At the end, maybe it's good that it's over for me. Right now, I think that I have to find to myself again and just trying to forget the clay-court season as soon as possible, and then reset and starting from the grass courts again."
Meanwhile, Petra Kvitova of the Czech Republic had a triumphant return, competing in a tournament less than six months after a knife attack at her home.
Kvitova, a two-time Wimbledon champion, beat 86th-ranked Julia Boserup of the United States 6-3, 6-2 in 74 minutes.
"I think it doesn't really matter how I played, but I won," the 15th-seeded Kvitova said. "I won already, before."
In another opening-day match, 2015 U.S. Open runner-up Roberta Vinci of Italy exited the French Open in the first round for the fourth year in a row.
The 31st-seeded Vinci, who became a household name when she ended Williams' hopes of a calendar year Grand Slam by beating her in the semifinals at the U.S. Open in 2015, lost to Rio Olympics gold medalist Monica Puig of Puerto Rico 6-3, 3-6, 6-2.