The Smoggies started the game unimpressively after Fran Villalba opened the scoring for the hosts in the 33rd minute off Maxime Colin’s assist.
Assombalonga then set up Daniel Ayala to level for the Smoggies with three minutes left to play before substitute Odin Bailey notched the match-winning goal in the 89th minute.
The 26-year-old DR Congo international featured for the duration of the game as Boro suffered their fifth loss of the season.
The defeat saw Jonathan Woodgate’s men drop to 20th spot in the Championship table after gathering 10 points from 11 games.
Assombalonga, who has four league goals this season, will hope to get on the scoresheet in their next outing against West Bromwich Albion on October 19.