Diouf was barracked by the Magpies faithful for a large proportion of the game but it was his two goals that made all the difference and gave the Wanderers their third away win in succession.
Newcastle had the better of the opening half and looked in firm control but Bolton came out in the second period a different side and where much more organised.
Sam Allardyce resisted the temptation to recall Quinton Fortune back to the starting line up and instead gave Tal Ben-Haim a chance to continue his good form at left back.
Diouf, Nicolas Anelka and Kevin Davies formed a three man attack with Diouf on the left, Anelka in the middle and Davies on the right but this was changed around for the final half and it worked in Bolton's favour.
A decision by the match officials caused much controversy in the 18th minute as Wanderers defender Abdoulaye Faye was penalised for handling an Obafemi Martins cross in his area but replays later showed the decision by assistant referee Glenn Turner was harsh.
Shola Ameobi scored the resulting penalty from the spot and although the Toon Army had most of the first half possession they rarely failed to threaten Jaaskelainen's goal until after the break.
One shot that the hosts did get on target was from defender Peter Ramage. Ameobi flicked the ball into the path of the young defender in acres of space but despite this he balooned the ball over the bar and was unable to increase Newcastle's lead.
Bolton's best chance of the half came moments before the Ramage incident when United goalkeeper Steve Harper managed to deny Kevin Davies after Nicolas Anelka's initial shot was blocked.
The start of the second half saw Newcastle come out of the traps lively enough but Bolton's Jaaskelainen did well to keep out a shot from Nigerian striker Martins which threatened to creep under him..
This miss proved to be costly for the Tynesiders as Bolton upped their game and posed much more of an attacking threat to what was a shaky looking Magpies back four.
On 55 minutes Bolton played themselves back into the game with a fine move which was finished off from close range by El-Hadji Diouf. Abdoulaye Meite delivered a pinpoint pass to Anelka on the left and the Frenchman showed clever control and passing to set up Diouf.
A minute or so later the former Liverpool man Diouf added his and Bolton's second when nodding in a flick on from Kevin Davies who had rose well to win Ivan Campo's deep free kick..
Emre flashed a shot wide from distance at the other end but it was the Wanderers who looked the more likely winners throughout the second half with Anelka showing much more prowess.
Kevin Davies was also in the thick of things for Bolton and his right wing cross was handled by Damien Duff in the area only for referee Alan Wiley to wave away the appeals.
Davies then clipped the top of the crossbar after receiving Anelka's excellent through pass but any goal would not have counted as the one time Southampton favourite was wrongly given offside as later was confirmed by television replays.
Anelka himself nearly got in on the goalscoring act ten minutes from time as he twisted and turned before lashing in a shot which nearly crept into the cormer of Harper's goal but Bolton had already done enough to secure victory.
A trip to local rivals Blackburn Rovers now awaits the Wanderers next weekend and this is then followed by a trip to bottom of the league Charlton in the next phase of the Carling Cup..
Bolton Wanderers: Jussi Jaaskelainen, Nicky Hunt, Abdoulaye Faye, Abdoulaye Meite, Tal Ben-Haim, Kevin Nolan, Ivan Campo, Gary Speed, Kevin Davies, Nicolas Anelka, El-Hadji Diouf (Stelios Giannakopoulos)
Subs Not Used: Quinton Fortune, Ricardo Vaz-Te, Idan Tal, Ian Walker
Newcastle: Steve Harper, Stephen Carr, Titus Bramble, Craig Moore, Peter Ramage, Nolberto Solano (Charles N'Zogbia), Scott Parker, Emre (Guiseppe Rossi), Damien Duff, Obafemi Martins, Shola Ameobi
Subs Not Used: Antoine Sibierski, Steven Taylor, Pavel Srnicek
Referee:
Alan Wiley
Attendance:
48,145
Booked:
Nolberto Solano (Newcastle)
Gary Speed (Bolton)
El-Hadji Diouf (Bolton)
Emre (Newcastle)
Craig Moore (Newcastle)
Kevin Nolan (Bolton)
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