World number 14 Maguire claimed a sixth ranking event and his first since he overcame Stuart Bingham 9-8 in the 2013 Welsh Open in some style as he slotted the final pink and black to edge a 42-minute epic 16th frame for title glory.
'The Maverick' moves up to ninth in the world rankings after wins over world number two Neil Robertson, world champion Judd Trump and Allen, the 2018 Masters winner.
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The Scotsman earns a £150,000 first prize, a £100,000 bonus for topping the money list over the three events sponsored by Coral – the World Grand Prix, the Players Championship and the Tour Championship – and a £10,000 cheque for a sparkling 139, the highest break of the seven-day event set during the final.
It is more than he won in his previous most lucrative season on tour when he trousered £230,000 in 2014-15. He moves onto £623,532 so far this season with the World Championship still to come next month.
Astonishingly enough, Maguire was only in the tournament involving the top eight in the world this season as first reserve with Ding Junhui opting not to travel from China.
"I actually don't know what to say because I wasn't good enough to be here," said Maguire, who has also won the Six-red world title and World Cup with John Higgins. "I managed to fluke my way to the title.
"I think over the last few years I just accepted that I wouldn't win a tournament again and it has kind of eased my expectations.
"I better not get carried away because I've won one trophy, but it is a great feeling. It's unreal.
"I've had a great season. This tops it off. I can't have any more confidence before Sheffield. I'm really excited about it."
Maguire will spend some of his money on the family and said: "I think everyone is after socks and shoes, we'll get some stuff like that."
Resuming at 4-4 from a taut afternoon session behind closed doors at the Marshall Arena in Milton Keynes, the Scotsman produced some trademark classy, power punching snooker to draw away from his close friend.
Maguire – who lost the UK Championship final 10-6 to Ding in December – set the tone in the evening with a lovely run of 139, the highest break of the week as he moved 5-4 clear.
The lead became 6-4 and could have been 7-4 only for Maguire to see a red drop in the pocket after slotting a blue that saw him stamp his cue in frustration.
Allen responded by contributing 64 to close to 6-5 behind, but Maguire would not be denied.
The 2004 UK champion refused to let that dishearten him as his focused attitude helped him reel off the next three frames including knocks of 78 and 53 to leave him on the cusp of victory.
Allen refused to buckle and missed the final pink on 107 with a possible 140 narrowly eluding him.
"I made too many mistakes tonight," said Allen, who collected £60,000 and moves up to number four in the world. "He played much better tonight and stepped it up. I felt like I missed the boat and should probably have had a lead after the first session.
"All credit to Stephen, he's been knocking on the door for a quite a while. If I'm going to lose to anyone, it would be to one of my best mates on tour. I'm pleased for him."
Maguire will hope to emulate this level of form when he heads to the Crucible Theatre to compete at the 44th staging of the delayed World Championship with begins on Friday 31 July in Sheffield.
FIRST SESSION REPORT
Mark Allen and Stephen Maguire are locked at 4-4 after an engrossing first session of the Tour Championship final in Milton Keynes.
2018 Masters winner Allen – who will rise to a career-best of four in the world rankings win or lose – led 2-0 and 4-3 behind closed doors at the Marshall Arena while Maguire held the lead at 3-2, but nothing will separate the two close friends when they play to a finish on Friday night.
The first player to 10 frames will win the tournament involving the top eight in the world this season.
World number 14 Maguire is bidding to claim his first ranking event since the 2013 Welsh Open and could land £250,000 if he lands the title – a £150,000 first prize and a £100,000 bonus for topping the money list over the three events sponsored by Coral, the World Grand Prix, the Players Championship and the Tour Championship.
If he loses he only trousers £60,000 – leaving world champion and world number one Judd Trump £100,000 richer due to the bonus money.
Allen thumped three-times world champion Mark Selby 9-2 in the last four on Thursday and made another vibrant start with 50 and 76 seeing him lead 2-0 before Maguire responded with knocks of 89 and 69 to restore parity at 2-2.
Mark Allen and Stephen Maguire.
Image credit: Eurosport
Allen rolled in a majestic knock of 125 after a stunning three-ball plant got the break started to level at 3-3, but he could not motor away from Scotland's 2004 UK champion Maguire as a few unforced errors from both men left the final finely poised.
They play to a finish from 7pm (BST) on Friday evening.
Tour Championship draw
Quarter-finals (best of 17 frames)
(All sessions start at 1:30pm and 7pm BST)
- Neil Robertson 5-9 Stephen Maguire (Saturday)
- Judd Trump 9-4 John Higgins (Sunday)
- Mark Selby 9-6 Yan Bingtao (Monday)
- Shaun Murphy 8-9 Mark Allen (Tuesday)
Semi-finals (best of 17 frames)
- Stephen Maguire 9-6 Judd Trump (Wednesday)
- Mark Selby 2-9 Mark Allen (Thursday)
Final (best of 19 frames)
- Stephen Maguire 10-6 Mark Allen (Friday)
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