The 22-year-old unleashed a spectacular long-range strike to secure the points for Rovers and leave Boro winless away from home in their last six games.
Middlesbrough caretaker-boss Mark Venus made two changes to the side that beat Doncaster, with Jozsef Varga and George Friend coming in while Blackburn were unchanged from the team that started at Blackpool last week.
The visitors were by far the most impressive side early on but it was Blackburn who forced the first save when Alan Judge's superb curling free kick was brilliantly tipped behind by Jason Steele after 12 minutes.
More than half of Blackburn's league goals this season have come from Jordan Rhodes and he would have had another but for a wonderful save by Steele after 37 minutes. Tom Cairney's in-swinging cross from the right found the striker who headed towards the goalkeeper's left but Steele somehow adjusted his body to claw the ball behind.
Boro responded minutes later through a flicked Jonathan Woodgate header but he failed to hit the target.
Middlesbrough were certainly tidier in possession but it was Blackburn who were the most incisive. They broke quickly and early substitute Josh Morris stung the palms of the busy Steele after 41 minutes.
The away side had to wait until the final minute of the first half to register their first shot on target as Rhys Williams floated in a deep cross for Kei Kamara whose downward header was scrambled behind by Jake Kean.
Blackburn were almost gifted a goal in first-half injury time when Grant Leadbitter inexplicably fed Joshua King whose ferocious strike was tipped behind by Steele.
Only three teams had scored more than Middlesbrough this season before the game and they showed their intent on the hour mark when Kamara's teasing cross into the corridor of uncertainty was heroically hacked away from Albert Adomah by Matt Kilgallon and, from the resulting corner, Marvin Emnes blocked Woodgate's goalbound header.
Rovers were incensed after 68 minutes when Kilgallon went down under the challenge of Woodgate but the referee was unmoved.
It required something special to beat Steele and Lowe duly provided it in the 76th minute with a thunderous 25-yard strike that flew into the top corner.
Boro tried to hit back straight away through Lukas Jutkiewicz who could only head over but it was Blackburn who finished the stronger.
First, Ben Marshall forced a smart low save from Steele after 87 minutes and a minute later Chris Taylor's low cross found Rhodes but he could only get a toe on it when sliding in and the ball rolled agonisingly wide.
The last chance fell to Jacob Butterfield but his fierce strike flew wide and Boro's chances went with it.