The German third seed's first grand slam match since triumphing at Melbourne Park in January ended in pain and despair as a shoulder injury prevented her from making much impact against hard-hitting Dutchwoman Bertens.
Kerber stepped on court wearing a striking black and white outfit but over the course of the next hour and 41 minutes, her mood had turned as grey as the dark clouds hovering over Roland Garros.
"I'm disappointed that I lost the first round here ... that was for sure not my best tennis I played today," the dejected 28-year-old, who took a medical time out in the third set, said.
"I tried to fight but she played good then in the important moments."
The result completed a hat-trick of losses for Kerber, who suffered back-to-back defeats in her opening matches in Madrid and Rome.
Bertens blindsided her opponent with some ferocious groundstrokes in the opening set.
While Kerber staged a comeback in the second, she struggled to get her shoulder moving in the third set and went off court for treatment when trailing 3-0.
"I start feeling the pain in the second set. It was getting worse and worse," Kerber said.
The unscheduled break failed to revitalise her, however, and after saving two match points, Kerber surrendered her title hopes with an ill-judged dropshot that failed to clear the net.
World number 58 Bertens, who won the Nuremberg title at the weekend, will next play either French wildcard Alize Lim or Italian Camila Giorgi.
Another former Melbourne champion, Victoria Azarenka, retired in her opening-round match with Italy's world number 118 Karin Knapp.
Fifth seed Azarenka quit with a knee injury down 4-0 in the third set having already saved a match point in a second set tie-break.