Having posted a modest 232, Otago rallied, picking up two quick wickets late on Sunday.
With overhead conditions greeting the teams yesterday morning, the home team would have been hoping to strike early.
Auckland resumed at seven for two with Tim McIntosh undefeated on five and Jeet Raval yet to face.
Raval prevailed despite doing his best to get out.
When play was abandoned for the day at 3.30pm, Auckland was 87 for two.
Otago's bowling attack, already well below full strength, suffered another blow with Jacob Duffy injuring his ankle after just one over on Sunday night.
He did not take the field yesterday and is expected to be out for two to three weeks.
That left Sam Wells and veteran left-armer Bradley Scott to shoulder the load with the new ball.
Scott turned back the clock with a wonderfully accurate stint.
The 34-year-old hit a perfect line and length and toiled away, bowling eight consecutive maidens.
It was not until his 54th ball - the last ball of his ninth over - he actually conceded a run, which was a push into the covers for a single.
Scott should have added to the two wickets he picked up on Sunday.
Raval got an edge which flew to wicketkeeper Derek de Boorder's left.
The gloveman made good ground but it bobbled out.
Once Wells and Scott ran out of steam, part-timers Jesse Ryder and Brad Rodden replaced them at the crease.
Rodden bowled as well as could be asked from a middle order batsman in his third first-class match.
He should have had Raval's wicket three times but each time the charmed left-hander had luck on his side.
Having already been dropped on 12 off Scott's bowling, he found a gap between Nathan McCullum at first slip and de Boorder, who was up at the stumps.
Four runs later, and on 34, Raval survived again with de Boorder shelving a tough chance while up at the stumps.
And just before the rain closed in, Raval was dropped again.
This time on 45 and by McCullum, who dived to his right.
Tim McIntosh stayed out of trouble but barely troubled the scorers either, reaching 28 form 125 deliveries.
Raval will resume today on 46.
