The winger scored in the 61st minute after Jamie McCart was adjudged to have handled his shot.
McCart then collected a second booking 15 minutes from time for sarcastically applauding the far-side assistant referee.
The result lifted Hibs back up to second on goal difference ahead of rivals Hearts in the cinch Premiership, while St Johnstone remain ninth.
Hibs started brightly and left-back Josh Doig was presented with the first opportunity after six minutes when Joe Newell's free-kick landed at his feet in a congested box.
But Doig's fierce drive from close range was repelled by Zander Clark.
Appeals for a Hibs penalty were then waved away by referee John Beaton moments later.
Kevin Nisbet tangled with goalkeeper Clark as the pair rushed to meet Ryan Porteous' low ball into the area but Beaton's whistle was silent.
Saints took their time to find their feet in the match but slowly began to enjoy more territorial possession.
Their first chance arrived after 18 minutes when Liam Craig played in a low free-kick to Chris Kane inside the area but the striker's turn and shot from a tight angle was comfortably palmed over by Matt Macey.
Visiting defender Shaun Rooney then lashed a volley wide from the edge of the box after another free-kick from Craig came back to him.
Macey was called upon again to get down to a deflected strike from Michael O'Halloran from 20 yards, with Porteous on hand to mop up the loose ball.
There were further chances for Hibs before the half was over but Boyle shot straight at Clark and Paul Hanlon headed wide from a Scott Allan corner.
Rooney had a good chance for Saints at the start of the second half when he drove into the box but the defender lacked composure when he hit his effort wide.
Hibs then took the lead in the 61st minute, with Boyle scoring from the penalty spot.
McCart blocked the winger's first-time drive inside the box but referee Beaton judged that he used his hand.
Boyle stepped up to take the spot-kick and squeezed a low drive past Clark, although the goalkeeper managed to get a hand to the effort.
McCart's afternoon was to go from bad to worse after the defender, having been booked for handball for the penalty, was shown a second yellow in the 75th minute.