Dhoni was accompanied by his wife Sakshi and cricketer friend R P Singh during the meeting at 10 Janpath, the official residence of Congress president Sonia Gandhi, a top BCCI source said.
"The appointment was taken earlier and the meeting was just a courtesy call," the source said.
Asked whether Dhoni also met Sonia Gandhi, the source said, "The appointment was only for meeting Rahul Gandhi."
Dhoni and Sakshi got married in a hush-hush ceremony on Sunday night at a farmhouse near Dehradun after getting engaged on Saturday.
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.
Congratulate MS Dhoni
BCCI ratifies charges against Modi
Pranab quits as Congress' West Bengal state chief
SA Prez invites Sonia Gandhi to watch Football WC
Spotted: Mahendra Singh Dhoni in Adelaide