The Lions and Blackburn looked set to settle for a point apiece until Ward adjudged Danny Shittu had tripped Grant Hanley in the area.
Millwall accused Hanley of a dive and implored Ward to consult his assistant, but the decision stood and Jordan Rhodes stepped up to score from the spot and secure a win for the visitors.
Jackett said: "That decision has cost us. I've just seen it again and it looked like a soft decision, in my opinion the referee got it wrong, it didn't look like there was any contact.
"I was looking for the refereeing team to make the right call as it looked soft at the time, and having seen it again it was."
Shittu's protests at the final whistle earned him a red card and Jackett added: "Danny's very upset but I have to back my player.
"He's a passionate man and he felt very passionately that there was no contact. Unfortunately it was a second yellow which we cannot appeal."
Karleigh Osborne's first goal for Millwall put them ahead, the defender finishing like a striker when he lashed the ball home from eight yards after Rovers failed to clear James Henry's free-kick.
Rovers levelled with a freak goal in the 56th minute when David Jones' corner deceived Rob Hulse on the near post, and goalkeeper David Forde, and squirmed over the line.
And 12 minutes from time Rhodes kept his head while all about were losing theirs, coolly sending Forde the wrong way from the spot for his 27th goal of the season.
- Sports & Recreation
- Danny Shittu
- Jordan Rhodes
- Grant Hanley