Vaughan, who has only just returned to the England fold after two knee operations, needed help from Jamie Dalrymple after limping through the early overs of his innings.
England management told reporters Vaughan had twinged his hamstring while fielding in New Zealand's innings, although he appeared to be rubbing his left knee when he came out to bat.
Vaughan missed more than a year of international cricket after surgery on his right knee but it was his 'good' knee that was troubling him on Tuesday.
He missed the Ashes Test series against Australia but was recalled for the triangular one-day series after passing a fitness test.
Vaughan was able to walk without problems but could not stretch out fully when running, prompting him to call for assistance.
The injury did not appear to effect his batting and he slammed three boundaries in making 17 off 29 deliveries when he pulled a short ball from James Franklin to Ross Taylor at midwicket.