But New Zealand recovered to 123 for three at tea on a rain-marred day after being sent into bat by England captain Alastair Cook.
Tom Latham was 51 not out and Brendon McCullum, the New Zealand captain, 41 not out.
Anderson removed both Martin Guptill, Latham's opening partner, and Kane Williamson for ducks to reduce New Zealand to two for two after the morning session was washed out without a ball being bowled.
Anderson needed just eight balls Friday to join the '400 club', reaching the landmark with a classic delivery that took Guptill's outside edge and was well caught, above his head, by second slip Ian Bell, who dropped a couple of chances during England's 124-run victory in the first Test at Lord's.
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No sooner had Anderson struck then rain forced a 10-minute stoppage.
But when play resumed, Anderson quickly had his 401st Test wicket.
Williamson, who scored a century at Lord's, was back on the ground where he had played for county champions Yorkshire.
Anderson had taken two wickets for no runs in three balls to leave New Zealand two for two in a match the tourists had to win to square the two-match series at 1-1.
For New Zealand, it was all to reminiscent of their second innings at Lord's where they slumped to two for nought and 12 for three.
England thought they had a third wicket on Friday when opener Latham, then on 18, was given out caught behind off Stuart Broad, only to overturn the decision on review.