With the top four riding line astern, Byrne continued to lead Hill, while Easton nudged ahead of Lowry on lap seven to assume a provisional podium position. Brookes, meanwhile, was slowly beginning to work his way into contention, an endeavour he eventually completed on lap fifteen as he cruised up to the back of Lowry's Honda.
With just five laps remaining to work his way to the front, Brookes immediately set about making his presence felt as he passed Lowry and Easton on successive laps to climb to third. Simultaneously, Hill had moved into the lead of the race again with a smart pass on Byrne with just four laps of the race remaining.
Seizing on his momentum, Brookes would also quickly find his way past Byrne for second, leaving him with just two laps to consider how to snatch the victory from Hill.
Entering the final lap, Brookes was on the tail of the Yamaha and appearing poised to launch an attack at the final corner Club chicane. However, a last gasp pass would not be required as Brookes instead dived beneath Hill at the start of the Campbell complex, nosing his GSX-R1000 ahead for the first time.
With just a few corners separating him from the chequered flag, Brookes held on for what is now his ninth career BSB victory and a return to glory at Thruxton, scene of his maiden win in 2010.
Despite missing out on another victory, Hill was satisfied with second as he lifted himself back into the reckoning, while Byrne crossed the line in third position to return PBM to the BSB podium on its return to the series.
Completing a very positive day for the former WSBK team, Easton chased his team-mate across the line in fourth position, while Lowry's fairly quiet run to fifth was nonetheless rewarded with the lead of the standings at the end of his breakthrough weekend.
A successful race for Padgetts Honda, Luca Scassa followed Lowry home in sixth – albeit 13 seconds adrift -, the Italian benefiting from Haga dropping back to tenth in the closing laps.
Between them, Jon Kirkham was seventh, ahead of pole sitter Lowes – who never recovered from a laboured start – and James Westmoreland.
Outside the top ten, Dan Linfoot led the BMW charge in 11th position, heading up the sole surviving MSS Bathams Kawasaki of Peter Hickman, while Michael Laverty paid for an early error as he could only manage three points for 13th place. Graeme Gowland and Chris Walker rounded out the points' paying positions.