The Magpies outside backs struggled under the high ball. Injuries also took their toll on the hosts with winger Mason Emerson forced off with a leg injury in the 11th minute, flanker Tony Lamborn with an arm injury in the 25th minute and No 8 Gareth Evans with a thigh injury in the 35th minute.
The Magpies were also on the wrong end of a 6-2 penalty count at halftime.
Hawke's Bay's 2016 club rugby MVP Neria Fomai started at centre for the Stags. He was forced from the field in the seventh minute with what appeared to be a concussion issue.
The Magpies opened the scoring in the second half with a spectacular try to winger TJ Vaega. It followed an outstanding burst from his brother and former Stags centre Cardiff Vaega and quality support from fullback Tiaan Falcon. West added the conversion.
Another Eade penalty in the 53rd minute had the Stags ahead 16-10. The Magpies took the lead for the first time in the 57th minute when Falcon won the chase to a clever kick ahead from TJ Vaega and West again added the extras.
Superb recycling play from the Magpies resulted in loosie Marino Mikaele-Tu'u scoring in the 68th minute. West converted and the Magpies led 24-16.
This try was scored while lock-flanker Geoff Cridge was in the sinbin. West was the Magpies player-of-the-match but only just ahead of veteran halfback Chris Eaton .
Former All Black Elliot Dixon was a workaholic at No 8 for the Stags. Props Joseph Walsh and Guy Millar also impressed during the first half.
Scorers:
Hawke's Bay Magpies 24 (TJ Vaega, Tiaan Falcon, Marino Mikaele-Tu'u tries; Ihaia West pen, 3 cons), Southland Stags 16 (Matthew Johnson try; Scott Eade 3 pens, con). HT: Southland 13-3.