Already with two goals to his credit, James raced clear of the Rovers defence and looked set to make it 3-1 when goalkeeper Steve Mildenhall dived to his left to parry his shot.
The striker was being chased by Rovers midfielder John-Joe O'Toole and Cooper was convinced there was contact from behind just as he was about to shoot.
"Luke was clipped and ended up striking the ball from an unnatural angle," said the manager. "In my eyes it was a clear penalty.
"I accept that it was a tough decision for the ref and I suppose if Luke had scored and he had pulled things back to award penalty we would have felt hard done by.
"But the challenge prevented Luke finishing as he might have done. He was outstanding and a hat-trick would have been just reward for his efforts.
"We have conceded a very late goal and it is a measure of how far we have come in recent weeks that my players are devastated not to have won the game."
O'Toole became even more of a villain as far as Pool were concerned when shooting a last-minute equaliser from a Lee Brown cross.
Matt Harrold had put Rovers in front with his first goal of the season on 35 minutes. The tall centre-forward, who missed a penalty in the previous game at Dagenham, controlled the ball on his chest before blasting a right-footed shot past Scott Flinders from just inside the box.
Before the cheers had died down, Hartlepool were level, James netting with a low right-footed shot from just outside the area with the home defence still celebrating.
On the stroke of half-time, man-of-the-match James netted again from closer range after Rovers had struggled to clear a Jonathan Franks cross.
Hartlepool had already hit a post through a Franks shot on 31 minutes and frustrated home supporters jeered their team off at the half time whistle.
But Rovers were far more purposeful at the start of the second period and came closest when Harrold deflected a shot from Eliot Richards onto the crossbar.