The home side declared at 385 for seven after lunch leaving the Kiwis needing an unlikely 321 to win from 48 overs to level the series at almost seven runs per over.
A shower delayed play for about an hour and the Kiwis should little appetite for the chase when they resumed in a match dominated by the bat on a lifeless pitch.
When stumps was called early with 20 overs left, the Kiwis were 104 for two with Ross Taylor on 36 and Kane Williamson on 32.
Having won the first Test by 208 run at the Gabba, the result means Australia have retained the Chappell-Hadlee Trophy.
Johnson, who announced his retirement from international cricket before the day's play, provided something to cheer about for the sparse final day crowd of just over 3,000 when
he claimed the wickets of both Kiwi openers.
He had Tom Latham caught on the fine leg boundary for 15, Josh Hazlewood sliding in to take a fine catch.
Johnson, 34, then surprised Martin Guptill (17) with a rising delivery and he fended a catch to Joe Burns at short leg.
Given a guard of honor by the Kiwis when came out to bat earlier in the day, the left-armer finished with 2-20 from six overs, a vastly improved return on his 1-157 in the first innings.
The two scalps saw Johnson finish his 73-Test career with 313 wickets at just over 28 apiece, the fourth best haul for an Australian bowler.

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