In addition to this, it also extended the Black Caps' lead over England to 171. There wasn't much play in the second session either before the final session was washed out.
Williamson (102) went past Martin Crowe's tally of 17 Test tons and now has most centuries for his country in the format.
Henry Nicholls was 49 not out while BJ Watling was on 17 as New Zealand reached 229 for four during the middle session of the day-night test before heavy rain swept across the ground. It seemed that New Zealand, too, might face a few problems when they come out to bat given England have a formidable pace battery with the likes of James Anderson, Stuart Broad and Chris Woakes in their side.
However, shortly after Williamson surpassed the triple-figure mark, England secured their only wicket of the day as James Anderson trapped the New Zealand skipper lbw for 102 off 220 balls, which included 11 boundaries and a six. There was one false start, with a resumption at 3.15pm announced, but rain returned immediately, and while there were periods when it was light, it never looked like disappearing entirely, and just after 6.30pm, play was called off.
Rain is forecast for each of the remaining three days.
Anderson has taken three of the four New Zealand wickets to fall so far in the Test but he conceded that his side were not unhappy to see the rain.More news: PUBG Mobile for iOS Launches in Canada
"But it was our job to make further inroads into their team and bowl them out cheaply". The two teams have acted like a couple who meet at the start of a rom-com and get on nearly too well - that was the one-day series - before discovering that in many ways they're a mismatch.
England were using an old ball in the only play under lights so far, on Thursday evening, but were unsafe enough to suggest the Black Caps could prosper in such a situation.
"We have to keep believing".
England's leading Test wicket-taker, with 526, said: "The pink ball is still in its infancy".
"As a swing bowler it's hard to take because it's hard to swing a ball that isn't round".