Allen and his co-drivers in the #55 Proton ORECA-Gibson 07, Fred Poordad, Francesco Pizzi and Porsche factory driver Gianmaria Bruni, were credited with a winning margin of just 0.016 seconds over the identical machine of Hanley, George Kurtz, Matt McMurry and Esteban Gutierrez.
Heading into the closing stages of the race, Allen had been third behind both Hanley and the AF Corse car of Matthieu Vaxiviere, clearing the latter with just seven minutes left on the clock before setting after Hanley.
Hanley had earlier rebuffed an attempted pass by Job van Uitert in the TDS entry at the inside of Turn 1, causing the Dutchman to spin.
Allen made his first attempt around the outside into Turn 1 at the start of the final lap, but the Australian had to regroup as 2020 Daytona LMP2 winner Hanley ushered him out wide.
The four-time race-winner in the European Le Mans Series, who was previously team-mates with Hanley at DragonSpeed in 2019, was able to slipstream the leader going through Speedway Turns 3 and 4 and barely nosed ahead at the finish for a memorable win.
"Honestly, I didn't really think we were in with much of a shot," reflected Allen.
"I was behind the AF Corse car for quite a while, and I could see the Crowdstrike car was building a gap more and more, so by the time I did get past the AF Corse car, there was quite a distance.
"But slowly but surely the gap kept coming down and I could see even from the penultimate lap I was getting a good run going to the start/finish line.
"I actually got in front before the start/finish line, so I thought, no point in trying to force the issue or take any crazy risk. [I thought] 'I've got the straight-line speed, I can do it still'.
"I did came out of the Bus Stop [chicane] thinking, 'Have I done this properly? Do I have enough time? Have I got an exit good enough?' And luckily I did, and just got him right below the line.
"I don't think I was breathing coming out of Speedway [Turn] 4 up to the start line!
"It was such a crazy moment for me. I don't think I've ever had anything like that, and I'm not sure I will ever again. It was really such an amazing feeling."
Proton's victory followed an incident in Thursday's second practice when Pizzi was at the wheel, which prevented the 18-year-old Formula 3 graduate from completing the night-time laps he needed to drive in the race after darkness fell.
Team owner Christian Ried said he was "super-proud" that his team was able to recover from such a setback to win on its prototype debut.
"It was quite a big hit in the barrier, and actually we need four new corners and a new gearbox and some body work," said Ried.
"We asked IMSA to get approved for working a little bit longer than 10:00, which IMSA is always super-kind to help.
"The guys worked until midnight and started in the morning at 6:00, and finally the car was not in perfect condition for the next session, but at least we could do a shakedown."
Referring to the Proton-run WeatherTech Racing Mercedes-AMG GT3 also winning in GTD Pro, he added: "There was not a lot of time for the guys to rest, so what they achieved with the GTD and LMP2 victory is just a great day."
