Recalled defender Matthew Connolly (pictured scoring) bagged the only goal of an injury-ravaged match as Boro slipped to a first league defeat in nine.
Connolly headed home Peter Whittingham's cross after 20 minutes in a fixture which saw five players substituted because of injury.
In spite of their impressive home record, the Bluebirds approached the game with two defeats from their last three outings and Malky Mackay made one change with Connolly coming in for injured full-back Kevin McNaughton.
Tony Mowbray also shuffled his pack with three changes from Boro's 3-1 success over Sheffield Wednesday.
In a frantic opening recalled Boro midfielder Seb Hines was booked for a rash challenge on Craig Noone before City were forced into a tactical reshuffle when centre-half Ben Turner limped off to be replaced by 18-year-old debutant Ben Nugent.
The home side edged ahead just before the 20-minute mark when former Arsenal man Connolly found space at the back post to head home his fourth goal of the season from Whittingham's right-wing cross.
Bluebirds boss Mackay was required to make a second change of the afternoon in the 26th minute minute when left-back Andy Taylor came off with a knock picked up early on to be replaced by Joe Ralls.
Middlesbrough captain Grant Leadbitter tested Cardiff goalkeeper David Marshall from long range before Boro were pressed into a substitution of their own on the half-hour mark when Richard Smallwood replaced injured Belgian midfielder Faris Haroun.
And Mowbray's men were almost on level terms moments after the switch.
Cardiff substitute Ralls fouled Emanuel Ledesma 18-yards from goal and the Argentinean midfielder picked himself up to strike a powerful, dipping drive which cannoned off the crossbar with goalkeeper Marshall beaten.
The visitors had another good opportunity to restore parity on the stroke of half-time.
Lukas Jutkiewicz's blocked shot rebounded into the path of Scott McDonald but the Australian striker fired over from inside the Bluebirds' six-yard box.
Boro made the stronger start to the second half and McDonald was again in the thick of the action driving straight at Marshall before heading wide from 12 yards.
Cardiff hit back and almost doubled their advantage when Whittingham's low free-kick from the right travelled through a crowded penalty area and almost caught out Boro keeper Jason Steele.
Mowbray introduced Marvin Emnes on the hour-mark as his side continued to search for an equaliser while Cardiff threw on Craig Bellamy in place of the injured Aron Gunnarsson.
Nicky Bailey then replaced injured Boro full-back George Friend before Emnes pressed Marshall into action with a snapshot from 12 yards which was tipped past the post.
The away side continued to dominate the second period without making their superiority count and Jutkiewicz blazed over when clean through as the Bluebirds hung on for victory.