McDonald made no mistake after 32 minutes to pounce on a defensive error from Hartlepool skipper Peter Hartley and fire clinically past Scott Flinders to hand City boss Steven Pressley a seventh point from nine in his first three games in charge.
Pressley made one enforced change to his side for the clash with Pool, bringing in Jordan Stewart to replace departed loanee Carl Dickinson at left-back.
It was Stewart who was required in the opening seconds when Charlie Wyke got around Aaron Martin down the left and whipped in a low cross that Stewart had to stab behind right infront of his own goal.
Beyond that the first half hour of the game was bereft of any real clear cut chances despite the Sky Blues continuing to come forward and try to play their way through a Hartlepool back four that seemed set up intenyt to try and get a point.
The game came to life in the 32nd minute though when a ball down the right flank from Carl Baker found Peter Hartley who was wrestled off the ball by McDonald, the City striker then closing in on goal before firing a finish past Pool 'keeper Scott Flinders and into the bottom corner.
The second half started off with more of a spark for City when Gary McSheffrey tried to loop an effort into the far corner two minutes after the restaart although his effort did not come down quick enough as it flew just over the bar.
Franck Moussa then forced a low save out of Flinders five minutes later when he burst into the area and poked a shot at goal, the Pool 'keeper getting down to save.
Flinders had to make a better save to deny Moussa two minutes later though when James Bailey played in his fellow midfielder who aimed his effort for the far bottom corner, Flinders saving with his legs to give City a corner.
It was Flinders to the rescue again after 73 minutes when a long-distance effort from Baker was beaten away by the 'keeper. The ball was pushed in to the path of McSheffrey though who got the ball stuck under his boot which gave the Pool back four time to scramble back and hustle the ball behind.
Hartlepool's first real flourish of the second half did not come until 11 minutes from time when substitute Luke James floated a ball into the six yard area for fellow sub Steve Howard whose header towards goal was batted away by Murphy.
It was the last real occasion that Hartlepool threatened the Sky Blues end though, not so for City as the Sky Blue Army saw Baker's mazy run on 90 minutes twist and turn three defenders before his final effort was turned away.
Attendance: 10,412 (272 away)
Coventry City: Murphy, Stewart, Edjenguele, Martin, Christie, McSheffrey (Bell 89), Bailey, Moussa (Fleck 78) , Baker (c), Jennings, McDonald (Wilson 70)
Subs: Dunn (GK), J Clarke, Barton, Willis
Hartlepool Utd: Flinders, Austin, Humphries, Collins, Horwood, Franks (Monkhouse 79), Walton, Poole, Sweeney (Howard 71), Hartley (c), Wyke (James 79)
Subs: McHugh (GK), Luscombe, Rutherford, Holden