The singer, who is on her “State of the World” tour, which stopped by Houston's Toyota Center Saturday night, was singing her hit song "What About" from her 1997 album, "The Velvet Rope."
As dancers behind her had just re-enacted a couple fighting, a fan's Periscope video shows Jackson’s pausing and shielding her eyes as she breaks down into tears, later clutching her knees.
"This is me," she said as fans encouraged her from the audience with cheers and applause.
Her rep did not immediately respond to ABC News' request for comment.
Jackson, 51, is in the midst of a divorce from estranged husband Wissam Al Mana. The two, who wed in 2012, welcomed a son together, Eissa, Jan. 3.
The last time the pop singer addressed her divorce was in May when she announced in a video that her tour would resume.
Jackson put her "Unbreakable" tour on hold last year when she became pregnant, later renaming the tour to "State of the World."
"I decided to change the name of the tour," she said then. "It's not about politics. It's about people, the world, relationships and just love."
In the video, she also acknowledged her split saying, "We are in court and the rest is in God's hands."
Earlier Saturday, Jackson was seen with her brother Randy and Houston mayor Sylvester Turner in Houston's George R. Brown Convention Center and NRG stadium, meeting with evacuees to offer words of support. The Jackson family was also accompanied by dancers and band members on the singer's tour.
The singer also dedicated the night's performance to those affected by Hurricane Harvey and encouraged fans to support local charities to support relief efforts. The proceeds from her Saturday night performance will also be donated to charity, according to a news release.