Wagner, the leading wicket-taker in the Plunket Shield for the past two seasons, picked apart the Auckland top order with an impressive 5-54 from his 21 overs, helping restrict the visitors to a first innings total of 221.
Auckland won the toss and decided to bat, but fell into trouble early on as Wagner, Jimmy Neesham and James McMillan restricted any of the visitors' top six from scoring more than 23 runs.
Anaru Kitchen battled his way to 74 while Bruce Martin provided some temporary support with a quick 31.
Otago raced out to 118-2 at stumps with Aaron Redmond reaching 72 and Darren Broom making 35 before both were dismissed off the bowling of Lachie Ferguson.
Meanwhile, Doug Bracewell took seven wickets as his Plunket Shield-leading Central Stags took control of the first day of their clash with Canterbury in Rangiora today.
After taking three top-order wickets before lunch, Bracewell single-handedly destroyed the tail as Canterbury were dismissed for 252 in 87 overs.
Bracewell finished with figures of 7-35 off his 19 overs and was responsible for picking up the last four wickets of the innings with a destructive display of swing, speed and movement off the pitch.
Tom Latham top scored for Canterbrury with 81 and was supported well in the middle order by Shanan Stewart, who made 61.
The Central Stags reached 32-0 before stumps with Jeet Raval (13) and Jamie How (19) at the crease.
At the Cobham Oval in Whangarei, Tim Southee picked up four wickets in his much-anticipated return to cricket for the Northern Knights.
Southee missed the Black Caps' tour of South Africa firstly for the birth of his first child and then a thumb injury, but came through unscathed today, picking up 4-97 from his 24 overs, as the Wellington Firebirds reached 412-9 at stumps.
For Wellington, Harry Boam scored 102, while Scott Kuggeleijn helped out in the middle order with a tidy innings of 74.
- Steven Holloway of nzherald.co.nz
