Sammy Ameobi scored the only goal of what was a tight match in the 71st minute.
Bolton entered the clash having lost just one of their last nine league fixtures on home soil, and ensured that they would jump from 22nd to 19th with all three points.
Bristol City would have gone third with a victory on the night, but a frustrating 90 minutes of action saw the visitors manage just three shots on target from 14 attempts.
After an uneventful start to the second period, Ameobi made the breakthrough in spectacular fashion - the 25-year-old netting after a fine solo run to register his first goal since October 2017.
Next up for Bolton is a home game against Fulham next weekend, while Bristol City will attempt to return to winning ways when they welcome Sunderland.
BOLTON (3-5-1-1): Alnwick; Beevers, Wheater, Dervite; Robinson, Vela, Henry, Osede, Little (Morais 79'); Ameobi; Walker (Clough 58')
BRISTOL CITY (4-4-2): Steele; Smith, Flint, Wright, Bryan; Paterson (Magnusson 65'), Brownhill, Pack (Diony 66'), Kent; Reid, Diedhiou (Engvall 86')