Lisowski was gunning for his first professional title and had a clear chance to win the deciding frame, but missed the final yellow off its spot. Maguire won a safety battle and cleared the colours to take the match. Victory for the 31-year-old Glaswegian is worth 2,000 ranking points as well as a £10,000 top prize.
Maguire came close to landing big titles last season, losing 9-7 to Ronnie O'Sullivan in the final of the German Masters and 10-9 to Peter Ebdon in the final of the China Open.
He admits this is an important season for him as he seeks to win his first full ranking event since 2008, and hopes a fresh approach to the game will pay dividends.
"I came to this event with a different attitude," said the World No 7. "I was willing to battle and play a safety game if I needed to. This season I'm going to try not to push the boat out too much. If it doesn't work then next year I'll go back to going for everything.
"I always start the season the same way, knowing that if I can get my name on a trophy I'll have done well. I don't count this in the same way as a ranking event but it gives me confidence and there are plenty of big tournaments to try to win.
"I think everyone has realised now that the ranking points from the PTC events are important. Plus £10,000 is a lot of money to be won in a weekend. It's easy to be up for it on the final day."
Maguire went 2-1 up with breaks of 84 and 75, Lisowski making a 70 in the second frame. The next two were shared then Gloucestershire's 21-year-old Lisowski came from 33-0 down to win the sixth frame and force the decider. From 42-0 down, Lisowski could have cleared up, but failed on the yellow on 56.
"He was a bit further away from the yellow than he wanted to be, but he still should have potted it," added Maguire. "Lucky for me he missed."
Lisowski had earlier beaten flat mate Judd Trump 4-3 in the quarter-finals and two-time world champion Mark Williams 4-3 in the semis. Maguire beat Australian Goldfields Open champion Barry Hawkins 4-3 in the quarters then saw off Andrew Higginson 4-1.
The Players Tour Championship is a series of ten events, four in the UK and six in Europe, with the top 24 on the final Order of Merit going through to the Grand Finals in March. They will be joined by eight players from the Asian PTC Order of Merit.