She did have some help during her 12-minute performance. Cee Lo Green, LMFAO, Nicki Minaj and M.I.A. also lent their talent to the halftime show.
However, it was M.I.A. who brought the controversy this year after flashing the middle finger to the crowd during the performance of Madonna's new single, "Give Me All Your Luvin."
In front of some 110 million viewers on NBC and uncounted others online, she made the gesture and appeared to sing, "I don't give a (expletive)" at one point, though it was hard to hear her clearly.
The NFL and NBC wasted little time in responding.
"The obscene gesture in the performance was completely inappropriate, very disappointing and we apologize to our fans," said Brian McCarthy, spokesman for the NFL, which produced Madonna's halftime show.
The screen briefly went blurred after M.I.A.'s gesture in what was a late attempt, by less than a second, to cut out the camera shot.
"The NFL hired the talent and produced the halftime show," NBC spokesman Christopher McCloskey said. "Our system was late to obscure the inappropriate gesture and we apologize to our viewers."
Janet Jackson's infamous oops during the 2004 halftime show raised a storm of controversy and put CBS in hot water with the Federal Communications Commission amid questions about the responsibility of TV networks to police their airwaves.
Justin Timberlake ripped off Jackson's bustier, exposing her breast for nine-sixteenths of a second, a moment for which CBS was fined $550,000 by the FCC.
After the M.IA. incident, McCarthy said the performer had not done anything similar during rehearsals and the league had no reason to believe she would pull something like that during the actual show.
The New York Giants beat the New England Patriots 21-17. The game is expected to challenge last year's record of being the most-watched U.S. TV event ever.
Madonna's performance was also carried live on SiriusXM Radio, giving the 53-year-old star the biggest single audience of her long-running career.
Earlier, Kelly Clarkson, Blake Shelton and Miranda Lambert offered some pregame patriotism. Shelton and Lambert did a twangy duet on "America the Beautiful" and Clarkson, in a simple black dress, sang "The Star Spangled Banner" without a hitch after last year's performer, Christina Aguilera, flubbed a line.
The Associated Press contributed to this report.