His dismissal came on the same day as former England captain Ray Illingworth warned Vaughan he was in no position to dictate his place in the Test side's batting order.
Vaughan, opening the innings as he has done recently for England, fell to New Zealand fast bowler Shane Bond, whose involvement in the Indian Cricket League has effectively ended his international career.
Last week Vaughan, again opening for Yorkshire, was caught behind for nought in a non first-class match off the bowling of Bradford and Leeds Universities' Harry Gurney and then fell for two in the second innings.
Vaughan has made it clear he wants to move back to number three in the England order in a straight swop with Andrew Strauss, who began his Test career as an opening batsman.
But fellow Ashes-winning captain Illingworth said Vaughan, who averaged only 20.53 in the three-Test series away to New Zealand earlier this year, badly needed a decent score.
"I hope Michael will lead us into next year's Ashes because, as a captain, he's our best bet to beat Australia," Illingworth, England skipper's when they triumphed away from home against their oldest foes in 1970/71, told Wednesday's Daily Mirror.
"But England have a big problem around the corner if he does not score enough runs because captaincy is a much harder job if things are not going well for you personally.
"He averaged only 20 in New Zealand and last week he made nought and two against a team of students and it's got to be worrying him a bit.
"That is not a very strong bargaining position if you want to change places in the batting order for England," the 75-year-old, chairman of selectors for three years during the 1990s, added.
Former Yorkshire and Leicestershire off-spinner Illingworth said fitness concerns regarding all-rounder Andrew Flintoff compounded the problems England had in deciding upon their batting order.
"It's a difficult one for the selectors, and it will become even more difficult when Freddie Flintoff comes back.
"You don't want to place too heavy a workload on Flintoff, so he will have to bowl as one of five bowlers rather than four.
"That means he will have to play at No.6 and a batsman is going to drop out.
"So I'm afraid Vaughan is going to have to come into the reckoning as a batsman and score some runs sooner rather than later."
England's three-Test home series against New Zealand gets underway at Lord's on May 15.