Amateur McPhail and the rest of the top 10 from the Fairhaven field of 121 will contest final qualifying next week.
McPhail shot a three-under par 69 to top the leaderboard by one stroke from a quartet of players on two-under: Adam Chapman of Penrith Golf Hub, Australian amateur Jasper Stubbs, fellow amateur Alejandro Rodriguez Andreu from Spain and the Huddersfield player Nick Marsh.
Only seven players shot under-par, including Lancastrians Jack Clarkson (Lancaster) and Mark Young (Longridge) on one under.
Qualifying in eighth and ninth on level par were Heysham's John Wilding and William Whiteoak of Ilkley.
The long day at Fairhaven went into overtime as a play-off was needed to decide the 10th and final qualifying place among the seven players who shot one-over par 73s.
And it was amateur Jake Hibbert of the Delamere Forest club who clinched the coveted spot.
In all 142 players won through at 15 venues around the UK and they will compete in final qualifying, taking place at four courses next Tuesday.
Three players will progress to The Open from each of the four, including St Annes Old Links. The other host courses are Fairmont St Andrews, Hollinwell (Nottingham) and Prince's (Sandwich).
Two Royal Lytham and St Annes players missed out on qualifying at Fairhaven by just one shot, Kieran Hogarth and Jamie Van Wyk finishing joint-17th on two-over.
The group on three-over included St Annes Old Links' Michael Kilgallon and Lytham Green Drive's Simon Wilson.
Harry Redman of RL&SA tied for 28th on four-over with Fairhaven's Daniel Morris.
Six-over and 46th was James Robinson of Lytham Golf Academy, while Fairhaven's Darren Carlisle shot eight-over, joining Blackpool North Shore's Curtis Thompson in a share of 68th place.
Harrison Thomas-Cooper from Old Links shared 78th spot (nine-over) with Lytham Green Drive's Michael Zwarts.
Jack Helm of Blackpool North Shore was 83rd on 10-over and Old Links' Jonathan Prescott a shot further back. RL&SA's Shamus Martin at least broke into the top hundred at 13-over.