The game a Bloomfield Road ebbed and flowed during the opening stages, despite the surreal atmosphere caused by vast numbers of Blackpool fans continuing to boycott games at Bloomfield Road in protest against controversial owner Owen Oyston.
Willock found the breakthrough and the 19-year-old midfielder's second opportunistic strike in the 37th minute effectively ended the contest.
League One Blackpool continued to press forward gamely but Alex Iwobi completed the scoring eight minutes from time.
Eddie Nketiah wasted two glorious chances inside the opening eight minutes, shooting into the side netting before stretching to prod wide.
Blackpool striker Armand Gnanduillet sashayed around a backpedalling Stephan Lichsteiner to shoot at Petr Cech but the visitors claimed an 11th-minute breakthrough when Aaron Ramsey's deflected free-kick hit the post and fell for Willock to nod in.
There were suspicions of handball against Alex Iwobi when he controlled to combine superbly with Carl Jenkinson, whose low cross was touched on by Nketiah for Willock to finish.
Cech's long punt found Nketiah, only for Mark Howard to save and compound the youngster's frustration.
Lichtsteiner was unable to cut out Marc Bola's 58th-minute cutback but fellow Blackpool full-back Michael Nottingham leant back to lift over.
It was an increasingly lackadaisical showing from Arsenal in the second half and Paudie O'Connor rose unchallenged to head a corner wide.
An injury to Howard brought Blackpool substitute goalkeeper Christoffer Mafoumbi into the fray and he was picking the ball out of the net with 10 minutes to play, although an offside flag denied Willock his hat-trick.
Mafoumbi could only parry Ramsey's shot across goal and the linesman's flag stayed down as Iwobi poached Arsenal's third.