Estre had a lead of just over six seconds in the #6 Porsche Penske as the German manufacturer engaged in a fierce battle with the Action Express Racing Cadillac halfway through the IMSA SportsCar Championship opener.
At the start of the 13th hour, Laurens Vanthoor in the #6 963 took the lead by staying in the car during the pit stop, while AXR lost time when Jack Aitken gave way to Tom Blomqvist.
The Swedish driver had only just slipped past Vanthoor when the 11th caution of the race was issued, while marshals scrambled to recover the #24 BMW of Dries Vanthoor, which had stalled on the track at the exit of Turn 3.
The subsequent pit stops changed the order, with Vanthoor regaining the lead from Rene Rast in the #25 BMW and Blomqvist in the leading Caddy dropping to third.
At the restart, Rast jumped on the Porsche and brought BMW to the front of the race and was even able to gain a small lead on his debut in the IMSA premier class.
However, Rast was unable to counter Blomqvist, who easily passed his BMW in the banked final corner, while Vanthoor's Porsche slipped down the order.
Blomqvist lost the lead again when he pitted at the start of the 15th hour and returned to the track 13 seconds behind the No. 6 Porsche, now driven by Vanthoor's teammate Estre.
The reigning Daytona winner reduced the gap to eight seconds when Estre made his own pit stop and joined the field in sixth, even behind Josef Newgarden's sister Porsche.
But Estre was able to overtake Newgarden and retake the race lead after Blomqvist returned to pitlane to hand the No. 31 Caddy to Pipo Derani, turning the race back in Porsche's favor.
The #40 Wayne Taylor Racing Andretti Acura, which had previously dropped out of the race, was now back on the lead lap, with Colton Herta helping it up to third in the overnight hours.
The Acura was in fourth place but moved up one place when the #25 BMW, which had briefly been in the lead with Rast behind the wheel, had to be taken to the workshop for repairs – a double blow for the Bavarian brand.
Newgarden dropped to fourth place in the No. 7 Porsche after his pit stop, ahead of the customer 963 of Neel Jani (Proton) and Tijmen van der Helm.
In the 14th hour, problems arose with the No. 01 Cadillac after Renger van der Zande came to a stop just before the exit of the Le Mans chicane, bringing up the 12th FCY of the race.
The car driven by Chip Ganassi was later retired at Daytona.
Era Motorsport leads in LMP2
Oliver Rasumssen brought the #18 Era Motorsport Oreca 07 back to the lead in LMP2 after overtaking the #99 AO Racing entry of Matt Brabham late in the 15th hour.
AO Racing had previously taken the lead with Paul Loup Chatin at the wheel, but their Oreca eventually fell to third behind the #8 Tower Motorsports car of Ferdinand Habsburg.
Ben Hanley brought the #2 Untied Autosports crew, which had led for much of the race, back to fourth place after taking over driving duties from Nico Pino.
Ferrari is ahead in GTD Pro
In GTD Pro it was Ferrari who were back at the top of the class thanks to a strong effort from Daniel Serra in the #62 Risi Competizione 296 GT3.
The Ferrari works driver overtook the #4 Corvette Z06 GT3.R of Tommy Milner to take the lead, while Sheldon van der Linde moved into third place in the #1 Paul Miller BMW M4 GT3.
Daniel Juncadella in the No. 3 Corvette was ahead of the trio but pitted late in the 15th hour and rejoined the field in fourth.
Mercedes took first place in the standard Pro-Am GTD class, with Indy Dontje in the No. 57 AMG GT3 leading the No. 32 machine of Kenton Koch.
The Inception McLaren, which was in the lead at half the race, has dropped to third place, with Ollie Millrow now behind the wheel of the #70 720S GT3.