In a game of few chances, Shields pounced on the stroke of half-time to earn the three points for the Tudors, with Spurs star Dele Alli watching on from the stands as he kept a keen eye on the progress of brother Harry Hickford.
The last meeting between the two sides had ended in a 7-4 victory for Eastbourne in the FA Trophy, but there was no sign of a repeat goal-fest this time around in a quiet start to the game.
After a very even opening 10 minutes, the first real shot of the match came from Graeme Montgomery as the Hemel winger lashed a volley over the bar from 20 yards.
It was Montgomery again who came close to breaking the deadlock in the 32nd minute but he was denied by a fine diving save from Lewis Carey, before the Eastbourne keeper did well again a moment later to deny Michael Richens.
Youngster Jack Kelly looked lively for Hemel at left-back, and he whipped in a cross on the stroke of half-time that was directed goalwards by Montgomery but easily gathered by Carey.
It looked as though the sides would go in level at the break, but Hemel had other ideas and broke the deadlock in stoppage time as Carey could only palm Nikolay Todarov’s shot straight to Sean Shields, who finished calmly to give his side the lead.
Hemel started brightly after the break and it was Oliver Thorne who had the first chance of the second half when his effort was deflected narrowly past the post, while Jamie Taylor was off target on the half-volley at the other end.
Kelly was next to try his luck with a fierce dipping drive that was tipped over the bar well by Carey, before Shields came close to bagging his second of the night as his effort whistled just past the upright.
Hemel began to drop deeper in an attempt to protect their lead, but in truth Eastbourne offered very little in the way of attacking intent, and the Tudors held on comfortably for the three points.
Borough are 11th in the table on 42 points from 33 matches while Hemel are one place above in 10th on 43 points.
Eastbourne Borough: Carey, Sheppard (Romain, 85 mins), Beale, Stone, Buckley, Khinda-John, Worrall (McCallum, 61 mins), Collier, Pinney, Taylor, Evans (Haysman, 76 mins). Subs not used: Simpemba, Lok.