Vaz-Te, who has been involved with the first team of late, struck with a header in the final minute to deny the FA Premier Reserve league leaders another victory.
The young forward also hit the woodwork early on in the first half with City's Danish goalkeeper Kevin Stuhr Ellegaard firmly beaten as the Wanderers looked to get their local rivals on the backfoot.
Chances where in high supply at both ends as Manchester City looked to press the Bolton goalkeeper Andy Oakes into action. Firstly the on loan stopper from Derby County was tested when faced with a shot from Christian Negouai but was able to watch as City midfielder Ian Bennett fired over the crossbar.
Blessing Kaku and Ricky Shakes both had good chances well saved by the City goalkeeper Ellegaard but the Scandanavian could not stop Wanderers opening goal on 20 minutes.
Salford born defender Danny Livesey recorded his first goal of the season when grabbing the final touch following a corner from Vaz-Te.
Negouai did his upmost to bring City back into the game but the former Charleroi player was twice thwarted by Oakes in the Bolton goal before Livesey almost netted a second goal with a carbon copy move of his opener.
Republic of Ireland youngster Joey O'Brien further tested Ellegaard with a powerful strike from distance but despite Bolton's best efforts they could not find a second goal before the interval.
The missed chances then came back to haunt Wanderers as Negouai finally netted an equalising goal ten minutes before half time. It was the least the midfielder deserved after an excellent performance.
Lively pair Vaz-Te and Shakes both had chances to pull the Trotters back in front in the second half but found City keeper Ellegaard on top form.
With eight minutes to go the City striker Bradley Wright-Phillips hit his fourth reserve goal in a week as the Mancunians looked to have sewn up victory before Vaz-Te's had the last word with his headed effort in the final minute and this was to cap off an exciting contest.
BOLTON RESERVES: Andy Oakes, Anthony Barness, Julio Cesar, Danny Livesey (Bradley Hill), Charlie Comyn-Platt, Ivan Campo, Blessing Kaku, Joey O’Brien, Ricardo Vaz Te, Ricky Shakes, Reda Kribib (Karl Luisi)
SUBS NOT USED: Dale Whitehead, Rhys Powell, Luke Magill
CITY RESERVES: Kevin Stuhr Ellegaard, David Sommeil, Sam Williamson, Jonathan D’Laryea, Paul Collins, Daniel Warrender, Ian Bennett (Michael Johnson, Stephen Ireland, Christian Negouai (Karl Bermingham), Bradley Wright-Phillips, Marc Laird (Ashley Grimes)
SUBS NOT USED: Kasper Schmeichel, James Lee-Matthews