Former Celtic star Hooper’s goal sparked jubilant scenes on the Canaries bench in contrast to the dejection of his one-time Parkhead boss Neil Lennon.
Indeed, Hooper had been a transfer target for Lennon earlier in the season so his winning goal was a double blow for the Ulsterman.
Graham Dorrans gave the Canaries an early lead as his right-footed free-kick deflected off Josh Vela into the net, but Adam Le Fondre looked to have rescued a point and extend their unbeaten run to four games.
Instead, Hooper lobbed keeper Adam Bogdan – as the Wanderers defenders switched off – to score an invaluable goal.
Lennon had promised his side would spoil a few parties in the remaining games of the season with Brantford and Bournemouth coming up in the next few weeks. That looked to be the case until Hooper’s strike made it five wins in the last six meetings between the teams.
Norwich made the perfect start with Dorrans’ deflected free-kick after Vela took down Nathan Redmond on the edge of the area.
The Canaries should have doubled their advantage six minutes later as Sebastien Bassong rose highest at a corner but cleared Bogdan’s crossbar by some distance.
And the visitors were in total control when Wanderers drew level totally against the run of play. It was so one-sided manager Lennon was poised to bring on Neil Danns to shore up his midfield.
Instead, youngster Tom Walker, who had been guilty of delaying a cross moments earlier, learned his lesson.
His flashing centre from the left picked out Le Fondre inside the six-yard box and the on-loan Cardiff City striker, back in the side after missing the Easter Monday trip to South Wales, finished with ease.
Walker continued to prove a threat to the visitors’ defence with his elusive running and was harshly booked for a foul on Wes Hoolahan.
Liam Feeney shot narrowly wide from another Walker cross that fizzed beyond three static Norwich defenders before the Canaries rediscovered their composure.
Top scorer Cameron Jerome, whose double won the reverse fixture at Carrow Road last October, brought a smart save out of Bogdan while the Hungarian international needed treatment after punching away another dangerous-looking Dorrans free-kick.
The second half was much more competitive and Wanderers were more of a match for their high flying visitors. So much so that Neil brought on Lewis Grabban after 57 minutes for Hoolahan.
And Grabban made an immediate impact, bringing out a save from Bogdan before Tim Ream cleared off the line from first-half scorer Dorrans.
However, Bolton had their moments going forward too with Le Fondre trying cheekily to chip John Ruddy while Alex Tettey cleared off the line after Dorian Dervite narrowly failed to connect with Walker’s corner.
Neil’s intention’s were clear and with 20 minutes left had made his full set of substitutions with Hooper replacing Nathan Redmond and Steven Whittaker going off for Ryan Bennett.
The visitors were incensed they did not get a penalty when Russell Martin’s cross hit Dean Moxey on the hand. But any ill luck was cancelled out in injury time as hot shot Hooper slotted his winner.