Matt Taylor fired the Premier League side ahead just before the half-hour mark before Maicon Santos levelled for Toronto on the stroke of half-time.
Jussi Jaaskelainen was Bolton's hero in the shootout as he saved two penalties.
Stuart Holden, Robbie Blake, Sean Davis and Gary Cahill had converted for Owen Coyle's men before Jaaskelainen guessed right to deny Oscar Cordon as Bolton secured a 4-3 shootout victory.
Manager Coyle was pleased with the signs of progress in his team, he told his club's official website: "It's been a fantastic tour and with each game we have stepped up the quality of our play."
He added: "There's no doubt that the clinical cutting edge will come as the pre-season games go by but equally we've learnt a lesson tonight.
"In injury-time we probably committed too many players in the box and we should have maybe settled for coming in at 1-0.
"We've still got a few rungs to go up on the ladder before 14th August but I've been delighted with the whole tour and with the performance tonight - it was a win-win situation."