"It was a rough and tumble race on a wet and sloppy track, actually, a beautiful thing to watch," Trump wrote, saying the decision "was not a good one."
"The best horse did NOT win the Kentucky Derby - not even close!" he added.
Maximum Security became the first winner disqualified for interference in the Derby's 145-year history, leading to an agonizing wait and an eventual stunning reversal that made 65-1 shot Country House the winner Saturday.
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.
Country House was dismissed as a long shot with a bad post on the far outside. It was only the chestnut colt's second win in seven career starts and his first stakes victory.
VIDEO: Kentucky Derby 1968: 1st winner disqualification in history
The Associated Press contributed to this report.