Ben Gerring had put the hosts in front on 10 minutes, with Aaron Lamont doubling the lead shortly afterwards, lofting his effort over ex-Town keeper Craig King.
However, City were back in the game early in the second half, Matt Paterson netting penalty and they were level on the hour when Sam Nombe curled home.
It was Nombe who scored again with 19 minutes to go, sealing an excellent victory for Musonda and his team-mates.
HATTERS RATED: Luton Town 0 Preston North End 1
Jones not worried if he never speaks to ex-Hatter Naismith again as long as the Hatters win at Bristol City
Ex-Spurs youngster reflects on 'bittersweet' Championship debut for Luton against Preston
Jones disappointed that Luton find themselves 'stretched' with injuries at such an early stage
Luton boss urges referees to do more in a bid to improve the flow of 'bitty' Championship matches
Keeper Harry Isted missed Chesham’s 3-1 Southern League Premier win at Frome due to injury, while Kavan Cotter and Jack James both started and played 90 minutes for Hitchin Town as they saw off Gosport Borough 2-1 at Top Field.
Robbie Burns put the Canaries in front on nine minutes, before ex-Luton forward Craig McAllister scored for the visitors.
However, the hosts won it with 10 minutes to go, thanks to Lucas Kirkpatrick’s strike.