Hearts appeared to be cruising towards victory after Craig Thomson, with a penalty, Rudi Skacel and Ryan Stevenson netted.
But Motherwell responded with three second-half goals, John Sutton netting headers either side of a Tom Hateley free-kick which evaded everyone.
Jefferies said: "It feels like a defeat. But I suppose I can balance it out with a lot of positives because it's probably as good as we've played in quite a while."
While Hearts had numerous chances to add to their tally - Stevenson twice hitting the post - they were also indebted to returning goalkeeper Marian Kello for keeping Motherwell at bay.
Jefferies added: "What a game Marian had. He didn't deserve to lose three goals."