The striker, a £15m signing from Nottingham Forest last summer, headed home from close range in the 90th minute after Jack Harrison’s effort had come back off the crossbar.
That goal cancelled out Marvin Sordell’s early opener for relegation-threatened Burton and earned Boro a valuable draw.
It was also Assombalonga’s first goal of 2018 and Boro boss Pulis hopes it will reignite the forward’s season.
Pulis said: “He’s got a goal now and that should spur him on. He missed a good chance earlier which he should have rolled in and you think it’s not going to be your day, but I’m pleased.”
Pulis had words of praise for his counterpart Nigel Clough, though, after seeing the struggling Brewers make things very difficult for the Teessiders.
“Nigel should get great credit for what he has done here with Burton in the Championship. It is fantastic with the budget and facilities he has got,” he said.
“I have watched a lot of Burton’s games this season and in every game they all turn up. We never got going today and they fully deserved to be winning.
“The players have got to understand that you have to turn up every week if you want to be successful in this league. It’s a great, competitive league and if you don’t turn up and give 100 per cent you will get turned over.”
For Clough it was another bitter end to an encouraging display after Sordell had swept home Lloyd Dyer’s cross early on to raise hopes among the Brewers that they could end their 15-game winless run on home soil.
“That game is right up there in terms of injustice,” he said. “Over the course of the game to not get three points after the level of performance and effort is extremely harsh on us.”
Albion worked hard to restrict Middlesbrough to few clear chances but they did not get the rub of the green when Harrison’s effort came back off the bar.
“If ever there was an instance of where the ball is not running for you and half an inch either way makes all the difference - which it did off the bar today - it’s an example of that. We feel that has been the case in a lot of games here this season,” Clough said.
“We contained Boro and I thought we looked a threat at the other end. To get to 90 minutes and with the nature and timing of the goal, it feels very unjust.”
Burton Albion: Bywater, Brayford, Naylor, McFadzean (Turner 90), McCrory, Sordell, Davenport, Akpan (Murphy 79), Dyer, Boyce (Allen 86), Bent. Unused substitutes: Samuelsen, Buxton, Sbarra, Egert.
Middlesbrough: Randolph, Cranie, Ayala, Gibson, Friend, Howson (Assombalonga 37), Leadbitter (Clayton 79), Besic, Traore, Bamford, Downing (Harrison 76). Unused substitutes: Konstantopoulos, Shotton, Fry, Baker.
Referee: David Coote (Nottinghamshire).