The Welsh side followed up their impressive 2-0 win at West Brom with a fine display on Teesside and are in a strong position as they enter the Christmas programme.
Former Rangers midfielder Chris Burke was the match-winner with a long-range free-kick in the second half.
Middlesbrough manager Gordon Strachan called for a more positive performance from his team after a rock-bottom midweek display against Blackpool.
His players responded with a more spirited display but it was not good enough to prevent another home defeat.
Boro boast an impressive away record but, unless they can end their dismal home record, they will struggle to seal even a promotion play-off place.
Middlesbrough were without injured skipper Gary O'Neil and recalled Marcus Bent to their attack.
Boro desperately needed a goal to boost confidence and Cardiff's defence blocked several shots in the early stages.
Middlesbrough had a scoring chance midway through the first half when Bent laid the ball off to Dave Kitson whose shot was blocked.
Cardiff suffered a blow when Peter Whittingham went off injured after 33 minutes.
City goalkeeper David Marshall produced a brilliant save when he flung himself to his left to keep a direct free-kick from Mark Yeates out.
Middlesbrough had enjoyed the balance of play in the first half but there was speculation about whether Cardiff would increase the tempo after the break.
The match-winning goal came from Burke direct from a long-range free-kick out on the left. The ball bounced in the six-yard box and past a motionless Bradley Jones into the far corner of the net.
Jones obviously thought one of his team-mates would go for the ball but he has to accept a portion of blame for the goal.
Middlesbrough hit back and were desperately unlucky not to equalise when, in a terrific goalmouth scramble, they struck the bar and had another effort cleared off the line.
There was a blow for Middlesbrough when England Under-21 international Adam Johnson limped into the dressing room. He must be a doubt for the north-east derby at Newcastle United next weekend.