This has been one rugged Triple Crown season for Baffert, who is recovering from a heart attack suffered while in Dubai in late March.
In the Derby, I'll Have Another ran down Bodemeister in the final 100 yards and won by 11/2 lengths.
Two weeks later in the Preakness, the result was the same, but by a neck.
Paynter drifted out a little near the finish in the 11/2-mile Belmont, and Union Rags got his neck in front at the wire, leaving Baffert a close-call loser again. It was another photo finish.
"Is there a Triple Crown for seconds?" Baffert asked. "I really thought he was going to win today. He was doing so well."
Baffert has won his share of classics - the Derby three times, the Preakness five times and the Belmont once.
Dullahan was a dull seventh as the 5-2 favorite.
"We just didn't have a finishing kick," trainer Dale Romans said. "This is a good horse, a very good horse. I was sure he was going to run a really big one."
So did the bettors, who made Dullahan a slight favorite over Union Rags.
Both Dullahan and Union Rags dropped back early. But that's where the similarities ended. While Union Rags picked up the tempo on the final turn, Dullahan stalled.
"Turning for home he just got to spinning his wheels," Romans said. "The race unfolded like it looked on paper to me."