Dhoni's cricketer friend R P Singh accompanied the couple in the meeting at 10 Janpath, the official residence of Congress President Sonia Gandhi.
"The appointment was taken earlier and the meeting was just a courtesy call," said a BCCI official.
According the sources, "The appointment was only for meeting Rahul Gandhi," not for Sonia Gandhi.
Dhoni and Sakshi got married on Sunday, Jul 4 at a farmhouse near Dehradun after getting engaged on Saturday, Jul 3.
The ceremony was a private affair with only close family members and friends in attendance.
The media was kept at bay by tight security during the marriage.