The game itself ended at 1-1 after full-time, but the Trotters where victorious in the resulting penalty shoot-out after City's Bradley Wright-Phillips blazed his spot kick over the crossbar.
Bolton captain Gary Speed had the best two chances for his side in the opening half, firstly he headed Ivan Campo's free-kick straight into the arms of the Blues goalkeeper Geert De Vlieger and then later saw his own free kick sail over the City crossbar.
Wanderers keeper Jussi Jaaskelainen then had to be alert to keep out a accurate Wright-Phillips shot shortly before the break, but he could do nothing about the opening goal in the 41st minute.
Veteran winger Trevor Sinclair found space down the right wing and immediatly whipped in a cross which was instantly converted by City's England U21 midfielder Joey Barton.
The extreme conditions throughout the game often meant that players had to take regular refreshments when there was a break in the play. The half time interval saw a number of changes occur, with Bolton bringing on Joey O'Brien and Jaroslaw Fojut in place of Speed and Tal Ben-Haim.
The Trotters where back on level terms just ninety seconds into the final period, as Kevin Davies scored his fifth goal of the pre-season with a first time shot past De Vlieger following a good lay off from Kevin Nolan.
Ricardo Vaz-Te (bar) and Henrik Pedersen (post) hit the woodwork for Bolton, and the lively City striker Wright-Phillips was once again thwarted by Wanderers custodian Jussi Jaaskelainen.
Tunisian defender Radhi Jaidi could have wrapped the game up for the Trotters in the closing stages, but he was to fire wide of De Vlieger's goalmouth meaning that the tie went to penalties.
In the resulting shootout Barton, Willo Flood, Sun Jihai and Karl Bermingham all scored for City, with Jay-Jay Okocha, El-Hadji Diouf, Ricardo Vaz-Te, Khalilou Fadiga and Ivan Campo doing likewise for the Wanderers.
Unfortunately for City it was Wright-Phillips, younger brother of recent Chelsea signing Shaun, who ensured that the Blues will face Everton in the Play Off game on Saturday afternoon as he blazed his penalty over.
Bolton on the other hand can look forward to defending their unbeaten start to the pre-season by taking on the Thai U23 team after they defeated Everton in a similar fashion earlier today.
Teams:
BOLTON WANDERERS
22 Jussi Jaaskelainen
2 Nicky Hunt
5 Bruno N'Gotty
26 Tal Ben-Haim
11 Ricardo Gardner
4 Kevin Nolan
16 Ivan Campo
6 Gary Speed
20 Ricardo Vaz-Te
14 Kevin Davies
9 Henrik Pedersen
Substitutes:
10 Jay-Jay Okocha for Nolan
12 Ian Walker
15 Radhi Jaidi for N'Gotty
21 El-Hadji Diouf for Pedersen
24 Joey O'Brien for Speed
30 Chris Howarth
31 James Sinclair
32 Jaroslaw Fojut for Ben-Haim
33 Johann Smith for Davies
39 Khalilou Fadiga for Hunt
MANCHESTER CITY
25 Geert De Vlieger
18 Danny Mills
27 Mikkel Bischoff
22 Richard Dunne
41 Stephen Jordan
8 Joey Barton
14 Kiki Musampa
6 Claudio Reyna
28 Trevor Sinclair
38 Stephen Ireland
42 Bradley Wright-Phillips
Substitutes:
1 David James
2 David Sommeil for Bischoff
3 Ben Thatcher
5 Sylvain Distin
17 Sun Jihai for Mills
31 Jonathan D'Laryea for Dunne
36 Karl Bermingham for Ireland
40 Lee Croft for Musampa
44 Willo Flood for Sinclair
45 Micah Richards for Reyna
Ref: Howard Webb
Bookmark or share this story with: