First five-eighth Josh Ioane is also likely to get some game time for Otago in the next few weeks.
Thomson, a 29-test All Black, last played for Otago in 2012 and after that played in Japan and Australia.
A spinal infection laid him low at Christmas 2017 and it appeared his playing days were over. But he slowly worked his way back into playing and has had some games in North Harbour club rugby of late. There was talk of him playing in the United States but visa issues were said to have put an end to that.
Otago Rugby Football Union general manager Richard Kinley confirmed Thomson would be with the squad for the next few weeks.
Thomson (37) has played 54 games for Otago. When he left Dunedin at the end of the 2012 season he said if he did end up coming back to New Zealand to play he would want to play for Otago.
Otago still has a few spots in its Mitre 10 Cup squad available and Thomson could fill one of those. His experience, nous and playing ability will be a valuable addition.
All Black coach Steve Hansen said in Wellington on Sunday Ioane would be sent to Otago to play while the team travelled to Perth, and then come back to play the Wallabies in Australia in Bledisloe Cup games.
Ioane was on the bench for the test against Argentina but did not get on. He did not make the playing squad for the drawn test against the Springboks in Wellington last Saturday.
With Bledisloe Cup games scheduled for August 10 and August 17, Ioane may not be required. Whether he makes the squad for the World Cup is up in the air but the All Blacks did take three first five-eighths to the 2015 World Cup.
Ash Moeke, who came into the squad last week to play North Otago, has left the Otago squad while Ben Miller, who played at first five-eighth against Thames Valley in the first game of the season, has been hampered by a knee cartilage issue and was due to have an operation this week.
Last year's captain, Michael Collins, was making progress with a long-term groin complaint and it was hoped he would get on the field soon.
Otago will play Tasman in its final warm-up game this Friday in Nelson. Its first game in the Mitre 10 Cup is against Bay of Plenty in Tauranga on August 11.