Thomson has recovered from a hand injury received when playing for the All Blacks at Carisbrook on June 13 and will take his position on the blindside flank.
Macdonald started on the bench behind Peter Mirrielees last week against Southland, but an impressive second-half effort against the Stags has put him into the starting line-up for the first game of the Air New Zealand Cup.
Thomson's inclusion is a bonus for Otago, and his availability sees Hoani Matenga moved to the reserves.
Otago coach Steve Martin had the luxury of having all players except injured prop Keith Cameron available for selection.
League converts Ryan Shortland and Michael Witt have failed to make the bench.
Glenn Dickson, getting over a shoulder niggle, is included in the reserves.
The other outside back reserve is veteran Luke Herden.
Ben Nolan and Sam Hibbard are on either side of Macdonald at scrum time, with veteran prop Kees Meeuws, named on the bench, and expected to come on in the second half.
It is the strongest side Martin could name and there is plenty of experience in the forward pack, with lock Tom Donnelly and skipper Alando Soakai both having played for Otago in previous challenges.
Otago last challenged in 2006.
Four University A players fill the inside back spots, with Andrew Parata and Brett Mather in the midfield, while Chris Noakes and Sean Romans will attempt to steer the side round the paddock.
Winger Fetu'u Vainikolo makes his Otago debut and much will be expected of Ben Smith at fullback, after an impressive Super 14 rookie year.
Martin said with little pre-season coverage of Wellington, there was not much to make of the opponent and Otago just had to stick to its own game.
He could sense a real hunger in the side and a determination from the players, and training had been going well.
"There is a real hunger from these guys to do well and to be as successful as they can. I'm not sure what Wellington will present to us but we are really focusing on our own game," Martin said.
He said it was great to have a near fully fit squad at this stage of the season.
The side will have a light training run at Carisbrook this morning, before flying to Wellington.
Wellington coach Jamie Joseph, despite having seven players away in South Africa, has named a strong side, with plenty of muscle up front, and speed at the back.
Jacob Ellison will captain the side from the loosehead prop position and will form an all Super 14 front row with Dane Coles and John Schwalger.
Jeremy Thrush will be looking for a big game after being ignored by the All Black selectors.
The Wellington team is without injured loose forwards Serge Lilo and Faifili Levave, while inside back Michael Hobbs is coming back from injury.
With former captain Tamati Ellison - Jacob's older brother - in South Africa with the All Blacks, Shaun Treeby and Robert Fruean form a relatively inexperienced midfield for Wellington.
Wingers Hosea Gear and David Smith will be dangerous for Wellington.
The match will be referred by the experienced Vinny Munro.
The forecast for Wellington tomorrow is for cloud with strong winds.
• Otago v Wellington Wellington, tomorrow, 7.35pm.
Otago: Ben Smith, Karne Hesketh, Brett Mather, Andrew Parata, Fetu'u Vainikolo, Chris Noakes, Sean Romans, Steven Setephano, Alando Soakai (captain), Adam Thomson, Tom Donnelly, Hayden Triggs, Sam Hibbard, Jason Macdonald, Ben Nolan.
Reserves: Peter Mirrielees, Kees Meeuws, Hoani Matenga, Paul Grant, Johnny Legg, Glenn Dickson, Luke Herden.
Wellington: Buxton Popoali'i, David Smith, Robert Fruean, Shaun Treeby, Hosea Gear, Daniel Kirkpatrick, Alby Mathewson, Mathew Luamanu, Scott Fulistaller, Victor Vito, Jeremy Thrush, Api Naikatini, John Schwalger, Dane Coles, Jacob Ellison (captain).
Reserves: Ged Robinson, Anthony Perenise, Daniel Ramsay, Masefau Leuluniu, Ruki Tipuna, Fa'atonu Fili, Alapati Leiua.
