Twice his thigh "fell apart".
But through it all, the 32-year-old never gave up hope of another chance on the test stage.
"That's why I play," he said. "That's why I kept going."
He got good wickets yesterday, but "to be honest I don't really care who I get out just as long as I get wickets. You're contributing to the team".
The words of one of his idols, whom he didn't name, rattled around in his head.
"You're lying if you say that you're a fast bowler and you say you bowl pain-free," he said.
South Africa's batting anchor, A.B. de Villiers, hit 83 but admitted he never felt "in".
"There's something in this wicket for the bowlers and you can't let go of your concentration for one minute. I won't say our top six failed, that would be very unfair to the [New Zealand] bowlers."
To that end, de Villiers was reluctant to talk about a fourth innings chase South Africa would be comfortable with.
"We'd like to get a couple of early wickets and make things a bit easier for us. The batters [on both teams] just haven't played well for a couple of days."
De Villiers praised Gillespie and fellow bowlers, and was proud of his own quick bowlers' work yesterday afternoon, when they put the skids under the batsmen for a second time.
"They stuck to their disciplines, had a lot of energy and consistent intensity."