The striker scored twice from the penalty spot, but also saw a spot-kick saved as Hibs created chance after chance.
Killie's Ryan O'Leary was also sent off late on for his foul on Donaldson for the third penalty.
Hibs started strongly. Rob Jones was just inches away from connecting with a header in front of goal before Filipe Morais' volley struck Steven Fletcher after good work from Ross Chisholm.
Killie almost snatched the opener when a 20-yard shot from Ryan Jarvis took a deflection and Yves Makalamby was glad to see the ball loop over his crossbar.
But Hibs grabbed the lead after 12 minutes after an instinctive strike from Donaldson. Killie failed to clear a Morais corner with any conviction and, after Brian Kerr played it back in, the Hibs striker reacted first to prod a ten-yard shot past Alan Combe.
Kilmarnock were unhappy that Jamie Hamill was down injured in the area after the corner but Stuart Dougal waved away Allan Johnston's protests.
Killie almost equalised immediately but Makalamby closed down his angles well to block Aimee Koudou's near-post shot.
Hibs dominated for long spells of the first half but Combe was well protected by his back four for the most part.
But the goalkeeper produced a magnificent leap to claw out a header from Jones which was bound for the top right-hand corner of his net.
Hibs were two up after half-an-hour from a hotly-disputed penalty. Referee Dougal ruled that Fraser Wright had fouled Donaldson in the penalty box when he looked to have won the ball and it sparked fury from Killie.
Simon Ford was booked and substitute Colin Nish was spoken to by Mr Dougal for remarks made to the stand side linesman as he was warming up behind the goal.
Donaldson kept his cool to send Combe the wrong way with the spot-kick and put Hibs 2-0 up.
But the Hibs' striker missed out on his hat-trick in the opening minute of the second half when his side were awarded a second penalty when David Lilley impeded him in the area.
He tried to clip the ball over Combe but the goalkeeper guessed right and managed to block his effort to keep his team in the game.
But Donaldson set up Mickael Antoine-Curier for the third after 65 minutes before Nish pulled back a goal for Kilmarnock when he touched in Willie Gibson's cross.
Donaldson then completed his hat-trick two minutes later when he was brought down in the area by O'Leary and sent Combe the wrong way again.