The Dark Blues dominated this one-sided contest but lacked a ruthless instinct, wasting much of their fine work up until the final third.
Fresh from triumph at Tynecastle just a few days earlier, McIntyre’s side had their sights set on securing back-to-back victories to enhance their hopes of Premiership survival.
But they were dealt a sucker-punch when David Turnbull converted a decisive 60th minute penalty after central defender Ryan Inniss’ moment of madness.
It was tough overall on the Tayside club who will revert to bottom-spot should rivals St Mirren get the better of Hibs this afternoon.
“To say it was frustrating is stating the obvious because we put so much into the game,” bemoaned McIntyre.
“We didn’t deserve to lose that game. In my opinion, we deserved to win it. But we didn’t punish Motherwell in the first-half when we were on top and paid the price for a bad decision in our own penalty box.
“In our position, we need points so you have to make better decisions and convert the pressure into points.”
Both sides enjoyed victories earlier in the week and Dundee’s 2-1 win away to Hearts had hoisted them off the foot of the table. Motherwell, having defeated Hibs 1-0, had to endure nightmare roadworks on their way to Tayside but eventually arrived one hour before kick-off.
Things were tight early on although Andy Dales, the on-loan Scunthorpe United winger, did see his shot fizz past Motherwell keeper Mark Gillespie’s far post, not long after team-mate Jesse Curran was forced into an early departure through injury.
Dales was forever busy, but his effort from 20-yards went abysmally over the bar when he ought to have at least hit the target after the visitors had decided to allow him ample space to pick his spot.
Team-mate Martin Woods pounced on yet more slack defending but he too was guilty of hitting a woeful shot harmlessly wide.
The absence of a killer touch afflicted them again on the stroke of half-time. Motherwell defender Charles Dunne was brushed aside allowing Andy Nelson a clear shot at goal, only for the former Sunderland striker to pull his effort well wide.
The second started with Dundee’s Craig Curran coming close from Nathan Ralph’s corner but the hosts were soon stunned.
From a rare flowing Motherwell move, substitute Elliot Frear was clattered into by Inniss in full view of referee Willie Collum.
Turnbull stepped up to ensure an expert job from the spot as his effort sent Seny Dieng, the home keeper, in the opposite direction.
Motherwell boss Stephen Robinson, whose side are now 14 points away from the relegation zone, said: “That’s our third league win in a row which is great. Dundee are a tough team fighting for their lives and made it hard for us.”