The pair will remain part of an expanded 30-man squad for the Tri-Nations tests against South Africa (September 12) and Australia (September 19), meaning both will miss Otago's Ranfurly Shield challenge against Canterbury on September 12.
They will also, assuming they are not released, miss Otago's game against Hawkes Bay in Napier a week later.
Thomson and Donnelly will at least get to play for Otago against Auckland at Carisbrook on Sunday before assembling with the All Blacks.
But the loss of the dynamic blindside flanker and the skilled lock will be a severe blow to Otago's hopes of winning the Shield challenge - its second in six weeks - and claiming a trophy it has not held since 1957.
Otago coach Steve Martin did not see much sense in lamenting the absence of Thomson and Donnelly for the Shield challenge, particularly as Canterbury loses seven All Blacks, including newcomer Colin Slade.
"We'd all like to have our All Blacks. I'm sure Canterbury would as well," Martin told the Otago Daily Times.
"But what we do now is go to our depth, and we're confident we've got some good young fellows who are raring to go."
After the Auckland game, Thomson's No 6 jersey will probably go to Hoani Matenga, though one of the No 8s - Steven Setephano or Paul Grant - could also move to the flank.
Otago lock Seko Kalou has been loaned to North Otago for its Heartland Championship game against Poverty Bay tomorrow, but he will rejoin Otago next week and probably join Hayden Triggs in the second row for the Canterbury and Hawkes Bay games.
Thomson has not played for the All Blacks since breaking a bone in his hand in the test against France at Carisbrook in June.
But it seems likely he will add to his 10 test caps, given Canterbury loose forward Kieran Read remains under an injury cloud.
Donnelly has been on the fringes of All Black selection for a while and it now seems a matter of when, not if, he gets his first black jersey.
Thomson and Donnelly, along with Canterbury utility Slade, were initially invited to a one-day training camp with the All Blacks in Christchurch on Wednesday.
Management later decided all three should stay with the squad for the last two home tests of the year as cover for injuries and to provide additional selection options.
All Black squad
For final two Tri-Nations tests
John Afoa, Dan Carter, Jimmy Cowan, Wyatt Crockett, Aled de Malmanche, Stephen Donald, Tom Donnelly, Jason Eaton, Owen Franks, Hosea Gear, Andrew Hore, Cory Jane, Jerome Kaino, Tanerau Latimer, Brendon Leonard, Richie McCaw, Mils Muliaina, Ma'a Nonu, Kieran Read, Joe Rokocoko, Isaac Ross, Sitiveni Sivivatu, Colin Slade, Rodney So'oialo, Adam Thomson, Neemia Tialata, Brad Thorn, Isaia Toeava, Piri Weepu, Tony Woodcock.
