The Otago left-hander appeared on track to post his seventh first-class hundred in the seven-wicket win against Canterbury but was caught and bowled for 96.
There was to be no repeat yesterday, as Rutherford brought up his 100 off 101 balls. He was out a short time later for 108, caught and bowled again.
But the 24-year-old has got himself into good touch before the test series against India this month.
Auckland resumed on 400 for seven and reached 467, Michael Bates chipping in with an undefeated 48. At stumps on day two, Otago was 280 for four thanks in part to Rutherford's efforts.
The Volts lost Aaron Redmond for 31 and Michael Bracewell (three) could not get established.
Rutherford and Neil Broom (28) added 81 for the third wicket and, at tea, the visiting side was 200 for four. Brad Rodden and Sam Wells continued the fight after the break, adding a further 80 in the final session.
Rodden, playing in his second first-class match, will resume on 34 with Wells (62) closing on a second consecutive century.
In Gisborne, a record seventh-wicket partnership for Northern Districts between Bharat Popli (82) and Mitchell Santner (118) left the home side in control of its encounter against leader Canterbury.
Once Popli was removed, ending the pair's resistance at 174, ND was eventually dismissed for 482.
Rain meant Canterbury's innings was called off at 16 without loss. Further rain is forecast for the Gisborne region.
In the day's other game in Napier, Central Districts was bundled out for 161 in reply to Wellington's 172. The visiting sides then progressed to 143 for three at stumps, a lead of 154.
- Otago Boys' High School will warm up for the regional finals of the New Zealand Community Trust Cup with a fixture against a Billy Ibadulla selection side at Littlebourne tomorrow.
The game should provide some stiff competition before the final against John McGlashan College on Waitangi Day.
- Additional reporting by APNZ.
