The Irishman made five birdies in a flawless performance over the Old Course at Sunningdale to hit the front at eight under, with defending champion KJ Choi and Thomas Bjørn just behind him.
Choi, who is bidding to become the first player to win back-to-back Senior Open titles in 25 years, had appeared set to lead the way at the halfway stage when he reached nine under through 14 holes but he made back-to-back bogeys at the 16th and 17th.
On a day of largely glorious sunshine, Bjørn – a fellow former Ryder Cup Captain – had earlier set the clubhouse target with a brilliant 63 that featured an eagle and seven birdies.
Justin Leonard surged into contention with a 65 to sit alongside Ernie Els, Ricardo Gonzalez and Cameron Percy in a tie for fourth at six under.
Harrington, who began the day four shots adrift of the overnight lead, opened with a birdie before a further gain at the ninth saw him hit the turn in 33.
He birdied the 11th to reach six under, and then quickly overcame the disappointment of a three-putt at the par five 14th to birdie the long par-three 15th, before adding a final flourish on the 18th green.
“I rode my luck a lot today,” said Harrington, who is bidding to emulate Bob Charles, Gary Player, Tom Watson and Darren Clarke as just the fifth player win both the Open Championship and Senior Open.
“Got my head in the game. Did a lot of good stuff mentally. Short game was sharp.
“I did a good job, where I should make a score score, and then I got in trouble on plenty of other holes.
“Hit some recovery shots and managed my game, but I never showed much confidence out there at all in my swing.”
For much of the afternoon, Choi, who won at Carnoustie 12 months ago, appeared in complete control as he made three birdies over his opening six holes.
A first bogey of the day came at the ninth for the South Korean, but he responded with three birdies in a four-hole stretch from the 11th to the 14th to briefly move two shots clear.
However, an errant tee shot in a fairway bunker resulted in a dropped shot at the 16th and he three-putted the 17th to drop back to seven under, before he showed a touch of class to get up and down from a greenside bunker at the last to save par.
Bjørn suffered a frustrating finish to his first round, but he used that to fuel his determination on Friday, matching the lowest round of the week so far.
The Dane, among the morning wave, birdied four of his opening five holes, before picking up another at the short par four ninth to turn in 30.
He chipped in for eagle on the 11th, before a birdie at the 15th saw him take the lead on the course, and while there was disappointment with a pair of bogeys at the 17th and 18th, there was further joy to come with a closing birdie.
“I just got out here in that mode of I know I played well yesterday and I was hitting the ball well,” he said.
“I knew I was playing well but I was just angry. Just angry.
“I wanted to get off to a start and hit a great shot on two, which it’s not like a given birdie, and then I hit some good shots from there.”
