England went into the match having already won the Six Nations crown, but they were denied a second consecutive Grand Slam and a record-breaking 19th successive Test victory by a ferocious Ireland performance in Dublin.
Jones acknowledged that it was disappointing to fall just short of the record, which they jointly hold with New Zealand, but admitted that it was not his side's day.
"It just wasn't our day today. Ireland played very well. It was hard to get anything going and we struggled in the line-out and we struggled in the break down. They were two key areas in a game like today," he told reporters.
"At the end of the day, we're back-to-back Six Nations champions. It would have been great to be Grand Slam champions and world record holders but it wasn't our day and these things happen.
"Sometimes you play against a team that's better than you and they were better than us today. They were fantastic around the break down. It was still only 13-9 at the end of the game and we didn't play well."
The defeat is the first Jones has suffered since taking over from Stuart Lancaster after England's early exit from the Rugby World Cup in 2015.