Country House finished second in the slop before objections were raised, causing a 22-minute delay while three stewards repeatedly reviewed different video angles before they unanimously elevated him into the winner's circle.
It was a first triumph in the Churchill Downs showpiece for trainer Bill Mott and jockey Flavian Prat.
"The victor kind of pushed me sideways", Prat said.
Jockey Flavien Prat, who originated the claim of foul, also won his first Derby.
This controversy will no doubt overshadow the rest of the racing season, which continues in two weeks as Country House will try to become the second consecutive horse to win the Triple Crown after Justify by winning at the Preakness.
Leading up to the race, Maximum Security held 8-1 odds to win the race and was widely considered one of the favorites to win. No. 1 was Donerail in 1913, who went off at 91-1. The $132.40 to win was the second-highest payout in Derby history.
In an exultant suite, Jason Servis, the 62-year-old trainer of the surging Maximum Security, shared hugs and congratulations with his brother John Servis, who trained the 2004 Kentucky Derby victor Smarty Jones, and with Gary and Mary West, the Maximum Security owners whose fortune came via telemarketing.
'If you think the end of the Kentucky Derby was confusing now you know how the horses feel about the whole race, ' comedy writer Matt Goldich posted on Twitter.
Man Injured After Falling From Cliff Into Volcano Caldera in Hawaii
The park said the man was seriously injured but did not provide further details about his condition. Kilauea is the most active of Hawaii's five volcanoes, and one of the most active in the US.
"He started getting a little bit scared", Saez said.
Servis backed up his jockey, saying: "He's right".
Maximum Security finished first by 1 3/4 lengths.
"It feels pretty darn good", Mott said.
Maximum Security was eliminated from the race after replay review determined that the horse went out of its lane, impeding the running progress of another horse.
"We are exploring our options to appeal", West told the AP.
War Of Will appeared to be the main sufferer as Maximum Security veered from the rail to the centre of the course before getting back on an even keel.
"If the stewards say, "No, the best horse won" - then they leave it", Lawson said in a phone interview Sunday, referring to countries that follow what the IFHA refers to as "Category 1" rules for interference.