The Glovers came out second best in the first-ever league meeting between the two clubs.
Playing the first of two games in the space of 48 hours over the Bank Holiday weekend, it was a lethargic first-half with chances at a premium as both goals remained unscathed.
Clearly geed up following the break, Myles Hippolyte almost grabbed his first goal for the club whilst Josh Kelly rattled the woodwork for the visitors before a frantic five minutes leading up to the hour-mark.
Josh Smile started the frenzy as his free-kick - which was initially disallowed for offside - was given to be swiftly followed by a penalty for the Magpies just 60 seconds later.
Striker Jake Cassidy stepped up from 12 yards but was denied by a superb Stuart Nelson stop to keep it at 1-0.
Ticking into the final 10 minutes, substitute Danny Whitehall looked to put the game beyond doubt only for Courtney Duffus to notch his third of the campaign and setup a tense final few minutes.
Defender Luke Wilkinson was introduced as an auxiliary striker to mark an unusual first appearance for the club, but a dramatic equaliser wasn't to come as back-to-back defeats were inflicted.
Looking for an instant return to winning ways, Charlie Lee was handed a full debut on his first outing in BA22 as Darren Sarll also opted for a change in shape.
Having started in a 3-5-2 formation in the opening five fixtures, Town's boss swapped to a flat back four with a midfield diamond featuring Lee in front of the defensive line and Lawson D'Ath behind the strikers.
Dominating the early possession charts, Tom Whelan and Myles Hippolyte registered long-range efforts that didn't truly test Taye Ashby-Hammond in the visiting goal, before the Magpies almost took the lead in fortuitous fashion.
Winning possession on the edge of Nelson's box Jake Cassidy's quick-fire attempt took a wicked deflection that left the home keeper rooted the spot, only able to watch on as it flew inches wide.
Bathed in sunshine in South Somerset that was as close as either side came to breaking the deadlock in the first-half as the searing temperature was only matched with a lukewarm performance on the pitch.
Both defences reigned supreme as both attacks faltered, meaning the opening 45 minutes came and went with little to excite the crowd of 2,179.
With both managers seemingly making the most of the interval, it was an electric start following the restart with near misses at both ends.
Racing out the blocks, D'Ath almost latched on to Tom Whelan's through ball but with Ashby-Hammond only able to dive on the ball and parry, Hippolyte had a chance on the rebound with his shot that flew a yard over the crossbar more of a reaction than a measured strike.
As applause rippled around the ground following that near-miss, Alan Devonshire's side went even closer at the other when Kelly crashed an attempt off the crossbar after weaving in from the left wing.
Already with more action than in the entirety of the first-half the frantic tempo continued as the visitors broke the deadlock after some initial confusion.
Smile's free-kick took a nasty deflection which resulted in the ball nestling in the back of the net but despite the linesman flagging for offside, the goal was awarded after consultation between the officials with it eventually deemed Hippolyte was the unfortunate individual to have gotten the deciding touch.
As the home faithful debated the nature of the game's opening goal, the Berkshire outfit were immediately given a chance to make it 2-0 when Carl Dickinson was adjudged to have handled a cross.
Squandering the chance, Nelson guessed correctly to dive full-length and deny Cassidy from the spot to ensure the match remained in the balance.
With a raucous atmosphere cheering on the green and whites, D'Ath stung the palms of Ashby-Hammond with a shot from an acute angle preceded by substitute Rhys Murphy - back after a 10-day absence with a hamstring injury - curling a 20-yard strike over the bar as the final 10 minutes approached.
Keen to avoid a nervy conclusion, the Magpies doubled their advantage when Whitehall picked out the bottom corner from 25 yards only for the Glovers to issue an instant response.
Played through on goal, Duffus kept his composure to confidently beat Ashby-Hammond on 86 minutes but the clock got the better of the hosts who suffered a first home defeat of the campaign.
Yeovil Town: Nelson; Alcock, Skendi, Bradbury. Dickinson; Lee, Worthington, Whelan (Rogers 80'), D'Ath (Wilkinson 89'); Duffus, Hippolyte (Murphy 71').
Bookings: Lee 19', Whelan 76', Worthington 88'.
Subs not used: Brzozowski, Hutton.
Maidenhead United: Ashby-Hammond; Sheckleford, Ellul, Massey, Twumasi; Smile (Whitehall 71'), Davies (Comley 67'), Upward; Kelly, Cassidy, Mensah (Fenelon 77').
Bookings: Ellul 45', Cassidy 90', Comley 90'.
Subs not used: Keetch, Landers.