Sri Lanka were closing in on wiping out their 303-run first innings deficit with seven wickets in hand when Boult brought their cautious progress at Christchurch's Hagley Oval to a halt.
He removed the defiant Karunaratne for 152 and Niroshan Dickwella for four as Sri Lanka were reduced to 293-5 at stumps, still 10 runs from making New Zealand bat again.
Angelo Mathews is not out 53 with Tharindu Kaushal on five while Boult, New Zealand's chief wicket taker, has three for 62.
The left-hander had been under enormous pressure after making a four-ball duck in his opening bat when Sri Lanka were rolled for a paltry 138 in reply to New Zealand's 441 and were forced to follow on.
But he handled the occasion with aplomb as he easily surpassed his previous Test best of 85.
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