In the 100th League encounter between the two clubs Wanderers won at a canter thanks to two first-half goals.
And it was a memorable afternoon for Bolton's Mexican star Jared Borgetti.
The striker only arrived from Central America last summer but already this goal poacher supreme has found the net in the FA Cup, UEFA Cup, Carling Cup and now the Premiership.
Borgetti's opener late in the first half set Sam Allardyce's side on the way to their first Premiership success since beating Everton 4-0 back in mid-December.
For City fans it was further frustration at their unpredictable team, as last week's derby mauling of Manchester United quickly became a distant memory.
The visitors even fielded an unchanged side with Robbie Fowler again having to settle for a place on the bench.
Bolton, weakened by departures to the African Cup of Nations, had to drag Nicky Hunt off his sick bed to take his place on the bench.
Despite not being at full strength the hosts quickly settled into their game with Kevin Davies providing plenty of problems for youngster Stephen Jordan.
The home side even had to reshuffle in the 21st minute when Khalilou Fadiga picked up an injury and was replaced by Ricardo Vaz Te.
There was further concern for Wanderers boss Allardyce when Stelios clashed with Richard Dunne and both players went off to receive treatment for facial injuries.
Eight minutes from half-time Bolton made the breakthrough. Jordan looked at fault as the ball eventually broke to Borgetti to add the final touch inside the six-yard area.
The same player was then denied by David James but City's reprieve was temporary.
Stelios' free-kick deflected off Dunne and at the second attempt Kevin Nolan was well placed to get back on the goal trail.
Nolan then tried his luck from distance as Bolton attempted to wrap up the points by half-time.
City could only improve in the second half and they did, though without really troubling home keeper Jussi Jaaskelainen. And the home team was able to soak up the pressure without too many alarms.
Stuart Pearce eventually called for replacements, taking off Albert Riera and Andrew Cole for Fowler and Antoine Sibierski. But with a lack of service up to the frontmen City had no cutting edge.
Borgetti, who claimed he'd been elbowed by Dunne, eventually made way for home debutant Matt Jansen and received a great ovation from the Reebok faithful.
Jansen was soon in the action and created a chance for Nolan, but on this occasion the midfielder's shot went wide.
The match ended on a sour note when the usually placid Trevor Sinclair chased after Tal Ben-Haim, resulting in a caution for the ex-England man.