The 24-year-old claimed the wickets of Darren Stevens (118) and Matthew Walker (87) before West Indies all-rounder Dwayne Bravo (23) also fell to Arafat.
Fourth-placed Kent, replying to the second-placed hosts' first innings score of 399, closed on 295 for six - having found themselves in early trouble at 34 for three.
Ed Joyce scored 158 not out to help Middlesex's bid to move off the bottom of Division One.
The visitors slipped to 56 for two after captain Scott Styris had chosen to bat in the match against Warwickshire at Edgbaston.
But Joyce led the revival as Middlesex closed on 344 for five.
The 27-year-old shared in stands of 71 with Nick Compton (52) and 82 with Jamie Dalrymple (43), while debutant Paul Harris and fellow South African Neil Carter each took two wickets.
Former Zimbabwe Test player Andy Flower made an immediate impression on his return to the Essex line-up on day two of the match with Gloucestershire at Bristol.
Flower, back in the side after a back injury, made an undefeated 114 as the visitors reached 265 for four.
Flower put on 111 for the third wicket with Mark Pettini, as the visitors sought to overhaul Gloucestershire's first innings score of 394.