It took Wanderers just 23 seconds to gain the upper hand at The Valley when Henrik Pedersen fired the ball past Charlton goalkeeper Dean Kiely following a good flick on by Kevin Davies.
The conditions in South East London made life very difficult for both sides to play fluently, the rain lashed down over The Valley and wind was also causing the players problems.
Former Wanderer Claus Jensen had the Addicks first chance of the game on five minutes when his shot came back off the crossbar after a good ball from former West Ham United player Paolo Di Canio.
Jensen then turned provider on 11 minutes when he set up striker Jonatan Johansson for the qualiser following a fine move. His inch perfect cross was headed home by the Finn who stooped to put the ball past countryman Jussi Jaaskelainen in the Bolton goal.
The Trotters where then forced into a change on the quarter hour mark after winger Stelios Giannakopoulos picked up an injury and former AC Milan man Ibrahim Ba came on to replace the Greek International in the midfield.
Both Kevin Davies and Kevin Nolan then had shots blocked for the Wanderers whilst Per Frandsen blazed over from 25-yards. However the first half saw chances very few and far between and the Addicks seemed to have the upper hand in terms of possession.
Charlton where dealt with a major blow shortly before half time as midfielder Jason Euell was stretchered off with a suspected ankle injury and replaced by the on-loan Chelsea striker Carlton Cole.
Referee Andy D'Urso then blew for the half time interval much to the releif of both sides who where keen to see the back of what was a very unproductive first half in terms of chances.
The two sides picked up slightly in the early stages of the second half. Bolton youngster Nicky Hunt had the chance to open his goalscoring account for his hometown club following a good ball from substitute Ba, however the Westhoughton kid saw his shot finely saved by the Addicks keeper Kiely.
Henrik Pedersen then had the first of two chances to add to his tally for the day. First of all the Dane won a corner following good work from Per Frandsen and then made a superb run which was only thwarted by the heroics of the Republic of Ireland keeper Kiely. In between however Bolton had to be resolute defensively as Bruno N'Gotty was the hero for Wanderers as he blocked a shot from goalscorer Johansson on 55 minutes.
Trotters striker Kevin Davies, who was suffering slightly from the effects of a rib injury sustained in the midweek clash against Aston Villa then headed a cross by ex-Charlton player Anthony Barness into the arms of Kiely whilst substitute Cole was denied at the other end as Jaaskelainen saved well at the feet of the Chelsea star.
Davies was then brought off to be replaced by the on-loan Spaniard Javi Moreno but the Atletico Madrid striker didn't have much time to make an impact on the game. Charlton also made changes as Jensen made way for Paul Konchesky with just under 15 minutes to go.
The winner came on 78 minutes as Kevin Nolan took advantage of some sloppy home defending to fire a superb shot on the turn past Kiely after the Addicks had failed to clear a corner from Ivan Campo.
It is now three league wins in three for Wanderers who move up to 8th in the Premiership table which caps off a fine week for the Trotters who also progressed through to the final of the Carling Cup during midweek.