It was a fair result on reflection, with Alain Perrin's side having dominated the majority of the game and taking the lions share of the overall chances throughout the contest.
First half the Wanderers where on the back foot and Lyon looked to exploit the gaps down the flanks with the likes of Nadir Belhaj and Sidney Govou causing problems.
Also problematic was Ivorian striker Kader Keita but fortunately for the Wanderers the African had little end product to some excellent build up play.
Bolton had the first couple of chances of the contest in the opening minutes but these proved to be very few and far between in the first half.
Kevin Nolan saw his effort saved by the experienced Gregory Coupet in the second minute of the game and then the Bolton skipper lashed his shot wide a couple of minutes later following a long throw in by player/coach Gary Speed.
From there on in it was all Lyon, the French side looked dangerous on the counter attack and in possession and the Wanderers where unable to play with their usual fluency.
Giant defender Matheiu Bodmer saw his headed effort go straight into the arms of Jussi Jaaskelainen following Karim Benzema's curling delivery from the right.
On nine minutes the French side went even closer when Keita headed back off the woodwork after yet another Lyon break down the right flank.
The Wanderers had their goalkeeper Jaaskelainen to thank on a number of occasions throughout the ninety minutes with the rest of the back line looking less solid than in previous games.
Firstly the big Finnish custodian got across his goal well to deny a long range effort from Belhaj and then he came out of his goal to deny the long serving Govou in a one on one situation after Kim Kallstrom's through ball had split open the Bolton defence.
On the half hour mark Jaaskelainen was once again the hero for the English side. Centre half Abdoulaye Meite misjudged a cross field ball from deep on the right allowing Benzema a sight of goal but the Wanderers keeper proved why he is one of the best by denying the teenager an opening goal.
A rare Bolton attack ended with the ball being in the net but the officials ruled Nicolas Anelka's header out for offside. Ricardo Vaz-Te's overhead kick was well finished off by the French international but unfortunately the match referee had other ideas.
Eight minutes before the break Kallstrom showed Wanderers why he can be a threat from outside the box when weaving his way infield past the challenge of both Meite and defensive partner Gerald Cid.
The Swede hit the final ball straight at Jaaskelainen but Bolton boss Sammy Lee will not be happy at the laxed defending which came from his players.
Kallstrom was again allowed to worm his way into the penalty box with ease but Bolton had summer signing Gavin McCann to thank to putting in a tackle of the highest quality.
Headed chances then came at either end with Lyon forward Benzema somehow failing to hit the target following an excellent run down the right by Keita.
Cid had a similar opportunity for Bolton at the other end but the former Bordeaux centre back headed the ball over Coupet's crossbar.
Wanderers where releived to be in at the break goalless and to their credit they came out in the second half much more organised and less disjointed.
Lyon suffered a major blow at half time when their influential captain Patrick Muller was taken off injured. Youngster Sandy Paillot came onto the field to replace the Swiss international defender.
Bolton tested Coupet for the first time ten minutes after the restart but Nicolas Anelka could only fire his shot from the edge of the box straight at his international collegue.
The French where still dangerous in attack and Belhaji once again made Jaaskelainen work hard after Govou had managed to get away from Jlloyd Samuel.
McCann fired wide from distance for Bolton on the hour and a few minutes later set up a chance for Anelka which just eluded the former Arsenal striker at the far post.
Both sides began to make chances and ex-Liverpool and Aston Villa striker Milan Baros came into the fray for Lyon in place of the excellent Govou.
On 66 minutes the Wanderers took a quick free kick with Vaz-Te laying the ball off to full back Samuel who in turn unleashed an effort over the bar.
It was quite a decent effort from the former England U21 star when you consider that he has only scored three goals throughout the whole of his career.
Vaz-Te himself also had a good opportunity when working his way into the Lyon area but the young Portuguese forward saw his attempt saved by Coupet.
Lyon where bouyed by the introduction of Baros and the Czech Republic striker nearly got an assist to his name but Keita was once again wasteful when firing the ball high and wide.
With twenty minutes to go Jaaskelainen pulled off a double save of the highest quality denying substitute Ben Arfa on his left post and then denying Baros on the follow up when scurrying across to his right post
Bolton brought on James Sinclair and Stelios Giannakopoulos to shore up the right flank but neither player was able to make their mark on the game.
Baros pace was causing Bolton problems and both Jaaskelainen and Cid had to be alert to deny the striker from getting a clear shot on goal.
Dead ball expert Kallstrom hit the wall with a free kick in the 83rd minute but made no mistake three minutes later when winning the game and the Peace Cup.
Ben Arfa's long diagonal run when unchallenged by Sinclair and Meite and the midfielder was able to pull the ball back for the awaiting Kallstrom who saw his effort squirm under the body of the otherwise excellent Jaaskelainen.
It was a sad end to an excellent competition but a good test nonetheless against a very good side with bags of Champions League experience and success at domestic level.
Bolton will now travel back to the UK for friendlies against Hibernian and Tranmere Rovers next week.
Bolton Wanderers: Jussi Jaaskelainen, Nicky Hunt (James Sinclair), Abdoulaye Meite, Gerald Cid, Jlloyd Samuel, Ricardo Vaz-Te (El-Hadji Diouf), Gary Speed (Stelios Giannakopoulos), Gavin McCann, Kevin Nolan, Kevin Davies, Nicolas Anelka
Subs Not Used: Ian Walker, Ivan Campo, Danny Guthrie, Joey O'Brien, Abdoulaye Faye, Lubomir Michalik, Zoltan Harsanyi
Olympique Lyonnaise: Gregory Coupet, Francois Clerc, Patrick Muller (Sandy Paillot), Anthony Reveillere, Nadir Belhaj (Remy Loic), Kim Kallstrom, Matheiu Bodmar, Jeremy Toulalan, Keda Keita (Fabio Santos), Sidney Govou (Milan Baros), Karim Benzema (Hatem Ben Arfa)
Subs Not Used: Fabio Grosso, Joan Hartock, Anthony Mounier, Remy Vercoutre
Referee:
Choi Myung Yong
Attendance:
Booked:
Hunt (Bolton)
Meite (Bolton)
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