Iain Blair, the SPFL secretary, delivered the trophy via helicopter to Dens Park after their 2-1 victory against Dumbarton as a taut championship title race degenerated into mud-slinging.
Ian Murray, the Dumbarton boss, accused referee Bobby Madden of cowardice when ignoring a late incident when Kyle Benedictus wiped out Chris Kane in the penalty box, depriving the visitors of a second spot kick of the day. If converted this would have seen Hamilton Academical, who crushed Morton by a shock 10-2 scoreline at New Douglas Park, crowned champions on goal difference instead.
"Everyone in the stadium knew it was a penalty," said Murray, serving a touchline ban. "It's beyond belief that he missed it. In fact, you don't miss that - you just don't give it.
"The fact he didn't give it means it's all about Dundee winning the league. It's the easy option and it's happened time and again with Dundee this season. You get frustrated but when you speak out you get sent to the headmaster's office again but it must change at some point."
For his part, in addition to savouring his third successive personal promotion, Hartley hit back at Dumbarton and also raised questions about the professionalism of the Morton side who were defeated so heavily.
"The Hamilton result is such a strange one," said Hartley. "Morton beat us 1- 0 and they drew with Falkirk. When do you see a game finishing 10-2 on the last day of the season? You don't even see that in amateur football. If you're a professional team you shouldn't lose 10-2.
"I was angry with Dumbarton's comments last time about them being leagues apart. Now we are a league apart - we're in the Premiership and they're in the Championship."