MacDonald headed home a Dean Bowditch corner two minutes into added time as the 10-man Glovers fought back from 2-0 down.
His effort added to Adam Virgo's 86th-minute penalty after a double from Danny Ings had appeared to put Cherries on course for victory.
Cherries were forced into a late change after midfielder Anton Robinson withdrew from the squad due to his partner going into labour.
Harry Arter, who impressed in the 2-0 win at Notts County, came in for Robinson, while Warren Cummings returned at left-back.
Cherries weathered a couple of early free-kicks, with Shwan Jalal saving from Paul Wotton and Andy Welsh's drive deflected for a corner.
Danny Hollands squandered a glorious chance to nudge Cherries ahead, the midfielder heading wide with the goal at his mercy following an Arter free-kick.
Hollands then saw his goalbound header saved by Glovers goalkeeper Stephen Henderson before Nathan Smith's blocked from Steve Lovell's close-range strike.
Jonathan Obika was errant with a gilt-edged chance for the hosts, the Spurs loan man dragging his shot horribly wide when well placed.
Jalal beat away a thunderous low drive from Nathan Smith before Liam Feeney clipped wide after being teed up by Donal McDermott.
Henderson saved bravely at the feet of Lovell after McDermott had again split the Glovers defence, while Obika's shot was deflected past the upright as an eventful first half drew to a close.
Henderson saved unconvincingly from Ings after the striker had traded passes with Lovell and let fly from 20 yards before Jalal smothered Welsh's effort.
Paul Huntington, booked for his part in a first-half flare up with Hollands, received a second yellow card after body-checking the same player five minutes into the second half.
Cherries took the lead when Ings converted a 54th-minute penalty following an off-the-ball incident involving Adam Smith and Adam Virgo.
While referee Steve Tanner originally turned down Cherries' appeals for a spot kick after Adam Smith had gone to ground under a challenge by Nathan Smith, Virgo decided to take the law into his own hands and paid a heavy price.
Virgo was penalised for taking retribution on Adam Smith, the Glovers midfielder grabbing the Cherries defender by the shirt and trying to haul him to the floor. Eagle-eyed linesman Adam Watts spotted the infringement and Tanner awarded the penalty.
Ings doubled Cherries' lead after 67 minutes, the teenager sweeping home Feeney's inch-perfect cross after Jalal's superb throw had set the winger on his way down the left flank. It was Ings's sixth goal of the season Virgo threw Yeovil a late lifeline when he scored from the spot four minutes from time after Arter had been judged to have handled a shot from Bowditch before MacDonald headed home a corner two minutes into stoppage time to earn the hosts a point.
Cherries: Jalal, A Smith, Cooper, Pearce, Cummings, Feeney, Hollands, Arter, McDermott (Pugh, 68), Ings (Dalla Valle, 80), Lovell (Fletcher, 80). Unused subs: Molesley, Baudry, Purches, Thomas (g/k).
Booked: Arter, McDermott.
Glovers: Henderson, Alcock, Huntington, N Smith, Bowditch, Welsh (Tutte, 74), Ehmer, Virgo, Wotton (Gibson, 74), MacDonald, Obika (Williams, 80). Unused subs: Jones, Upson, Gritton, Stewart (g/k).
Booked: Huntington, Virgo, Ehmer.
Sent off: Huntington.
Referee: Steve Tanner (Somerset).
Attendance: 6,150 (inc 2,163 away supporters).