It was goalless at the break at Theobalds Lane but on the hour-mark Joey May broke the deadlock to give the visiting Urchins the lead.
May eventually doubled his and Hornchurch`s lead as stoppage time arrived, with George Pullen immediately reducing the arrears for the Ambers.
Thurrock missed the opportunity to move into third place as they were held to a 1-1 draw on their own Ship Lane patch by groundsharers Romford.
Ryman League
A 23rd minute Kamarl Duncan own goal gave the Boro a 23rd minute lead. But the `visitors` equalised 15 minutes from time through Ross Wall.
Tilbury were also looking to put pressure on the top five, but they also had to settle for just one point from a goalless draw in their home game against Maldon & Tiptree.
Harlow Town moved up to twelfth with games in hand on all above them after beating second-bottom Heybridge Swifts 3-1 at Barrows Farm.
But the Hawks had to come back from being a 26th minute Luis Morrison goal down to win. Crucially, Jared Small equalised right on the stroke of half-time.
And then 15 minutes from time Ryan Melaugh put the Hawks in front, with sub Joey Benjamin making the points safe with a third five minutes from the end.
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