Former Wanderers target Artim Sakiri forced Andy Oakes into a save early on but the Macedonian captain could not find enough accuracy on his low shot to trouble the Bolton keeper.
At the other end Albion's Polish goalkeeper Thomas Kuszczak was kept busy as a Blessing Kaku shot deflected wide and this was closely followed by an attempt from French youngster Bedi Buval who hit a neat shot on the turn.
Kuszczak's work was not done as he had to stay alert with a Khalilou Fadiga free kick and a long range effort from flame haired midfielder Dale Whitehead.
Bolton then suffered a series of injury problems, firstly Charlie Comyn-Platt had to leave the field temporarily to receive stitches to a head wound and he was closely followed by Andy Oakes who had a twisted ankle shortly before the break, if that wasn't enough striker Karl Luisi then departed the fray at half time to be replaced by central defender Jaroslaw Fojut.
These interuptions did not put Wanderers off course too much as they found themselves 1-0 up within five minutes of the restart. French defender Florent Laville capitalised on some indecisive defending to open the scoring for his first goal in Bolton colours.
Polish substitute Fojut then had a chance to further the Bolton lead but he was to unfortunately fire wide after being put in a good position by wing back Ricky Shakes.
Midfielder Sekou Berthe thought he had brought Albion back on level terms but his excellent drive was well saved by the Trotters substitute goalkeeper Chris Howarth.
The impressive Shakes then hit the winning goal for Bolton at the other end with a fine shot which was to leave Baggies keeper Kuszczak stranded.
BOLTON RESERVES: Andy Oakes (Chris Howarth), Rhys Powell, Bradley Hill, Florent Laville, Charlie Comyn-Platt, Dale Whitehead, Blessing Kaku, Khalilou Fadiga (Luke Magill), Bedi Buval, Ricky Shakes, Karl Luisi (Jaroslaw Fojut)
SUBS NOT USED: Craig Knowles, Danny Stott
ALBION RESERVES: Thomas Kuszczak, Bernt Haas, James Holmes, Robert Davies (Ezekiel Tomlinson), Sekou Berthe, Thomas Gaardsoe, Brian Smikle, Robert Elvins, Kyle Patterson (Jared Hodgkiss), Artim Sakiri, Lloyd Dyer
SUBS NOT USED: Matthew Jones, Forsythe, Kelleher