Jackson, signed in the summer from Gillingham, pounced with a tap-in a minute before the break for his fourth goal of the season to hand City a deserved half-time lead.
Middlesbrough, without an away league win since April, nearly snatched an equaliser in injury time but substitute Scott McDonald fired wide.
For Norwich, it was their first home win over Boro since 1986 while the visitors will now look to appoint a permanent successor to Gordon Strachan with the fans chanting the name of former defender Tony Mowbray during the game.
Norwich manager Paul Lambert responded to the 2-1 midweek home defeat by Crystal Palace by making three changes.
Elliott Ward returned from suspension to replace Jens Berthel Askou at centre-back while midfielders Anthony McNamee and David Fox came in for Wes Hoolahan and Korey Smith.
Luke Williams and Kevin Thomson replaced Mickael Tavares and McDonald as Boro caretaker manager Steve Agnew made two changes to the side which went down 1-0 at Nottingham Forest on Tuesday.
Matthew Bates and Leroy Lita, who had previous loan spells at Carrow Road, started for the Teesiders, winless on the road this season.
The Canaries were backed by their biggest crowd of the season as they attempted to bounce back from the disappointing defeat to Palace, their second home loss in three games.
They had the first opportunity in the ninth minute when McNamee whipped in a corner which Boro failed to deal with and the ball fell to Ward, who could only scoop his effort over the crossbar from six yards.
Gary O'Neil curled a 30-yard free-kick into the hands of City goalkeeper John Ruddy in a rare opening for Boro but it was the home side who continued to create chances.
Captain Grant Holt fired wide from 25 yards and strike-partner Jackson blasted over from 12 yards, sandwiching a Lita header which went over from O'Neil's corner.
But Norwich were unlucky not to take the lead in the 25th minute. Again Boro failed to clear a McNamee corner and when the ball found Andrew Crofts, his shot on the turn hit the inside of the far post and went into the grateful arms of Boro goalkeeper Jason Steele.
Jackson volleyed another opportunity over from Russell Martin's cross as the Canaries continued to press for the opener.
Nicky Bailey drilled wide for Boro from 30 yards while Crofts was also wayward with an effort from just outside the box before the visitors lost injury-hit Kevin Thomson four minutes before the break as he limped off.
Norwich deservedly went in front a minute before the break. McNamee delivered the ball to the far post where Holt knocked down for Jackson to have a simple tap-in.
The second half was largely forgetful with Lita heading wide a Tony McMahon cross with 16 minutes left for Boro, who then had a decent chance to equalise in injury time but McDonald shot wide from six yards.