Truro ramped up the pressure on the hosts as Tyler Harvey and Cody Cooke ballooned over when well placed while Andrew Neal headed straight at Jonathan Miles.
Former Margate defender Ben Gerring was then inches away from scoring against his former side, only to see Chris Sessegnon hack his header off the line.
However, Neal got his side level late in the half as he snuck in behind the Blues defence and poked a shot underneath Miles.
Akindayini quickly wrestled the lead back for Margate early in the second half when he belted a beautiful half volley from the corner of the box into the far corner of the net.
Miles kept his side ahead midway through the half with a comfortable save to deny Cooke, while he flew full stretch to palm away Jamie Richards long range strike.
Margate nearly made it more comfortable as Ben Swift scored late in the game as Tom McHale spilt Dave Martin’s free-kick but it was adjudged offside.
Margate: Miles, Seesegnon, Palmer, Rogers, Moore-Azille, Swift, Akindayini (McFarlane 88), Evans, Gueye (Tumwa 90+3), Morgan (Ngamvoulou 65), Martin. Subs not used: Pajetat, Hamilton.
Margate Man of the Match: Daniel Akindayini