The Glovers dominated proceedings but came away empty-handed from their trip to Lancashire in Sky Bet League Two.
In an opening 45 minutes full of action Town started the brighter but were dealt a blow when AJ Leitch-Smith opened the scoring against his former employers midway through the half.
It could've got worse 10 minutes later when the hosts were awarded a penalty but Nathan Baxter kept out the striker's attempt before the visitors ended the half in the ascendancy looking for an equaliser.
However, the Shrimps doubled their lead on 48 minutes through Rhys Oates to put themselves in the driving seat, before Olufela Olomola reduced the deficit with a little over 20 minutes remaining.
Town continued to dominate but a string of fantastic saves and the post denied Darren Way's side a share of their spoils that their performance merited.
After an enjoyable trip to Carlisle last weekend Town's boss made three changes for the second long away journey in a row.
Picking up a virus in midweek, top scorer Alex Fisher remained at home to allow Yoann Arquin a starting berth up front, with two further changes in midfield.
Having come on to mark his return from a two-month injury last weekend, Wes McDonald was re-introduced to the starting eleven in place of Omari Patrick who took a seat amongst the substitutes, with Jake Gray swapping places with Alex Pattison in the middle of the pitch.
Completing the matchday 18, club captain Francois Zoko was involved for the first time since the second game of the season to start on the bench.
Showing no signs of lethargy following the 250-mile trip to the North West the green and whites started in a sprightly manner by winning a couple of corners after good work by Rhys Browne on the right wing.
Sensing the first chance of the match would fall the way of the visitors, it did after 14 minutes.
Brimming with confidence following his winner last Saturday, James started a move that almost culminated with a second goal in as many games.
Browne's cross picked out the defender at the back post but his stooping header flew into the advertising hoardings immediately behind the goal as it just about stayed goalless.
Having taken charge of proceedings in the first-half the Glovers looked in control but were dealt a sucker punch on 23 minutes.
With the Shrimps yet to test Baxter they took the lead with their first meaningful attempt on goal courtesy of former Town striker AJ Leitch-Smith.
Receiving the ball in the box Morecambe's top scorer turned neatly before picking out the top corner for his fifth of the campaign.
Buoyed by taking the lead Jim Bentley's side pressed for a second and 10 minutes later had the chance from the penalty spot after Aaron Wildig went down in the box.
Leitch-Smith stepped up but Baxter guessed correctly to get two strong hands to the strike and keep the score at 1-0.
A potential turning point in the match the visitors enjoyed some good fortune as Vadaine Oliver's header was ruled out for offside, before Darren Way's side looked to strike back before half-time with some late pressure of their own.
Winning yet another corner, Gray's delivery worked its way to Bevis Mugabi whose volley into the floor was brilliantly tipped over by Mark Halstead.
Continuing to press, Browne had a handball claim waved away by referee Peter Wright before firing a dipping volley from 20 yards just over as they had to settle for a 1-0 deficit at the halfway stage.
Needing to carry the momentum they ended the first-half with the green and whites found themselves 2-0 down just three minutes after the restart.
Oates drove at the back four before pulling the trigger from 25 yards with a strike that skipped off the surface to beat Baxter and nestle in the back of the net.
Needing a strong response the Glovers almost got it inside a minute when Olomola turned cleverly in the box prior to driving a strike just wide of the post, as Way introduced Pattison for Gray from the bench.
Looking for a repeat of his set-piece success at Carlisle a week previous, James saw a 30-yard free-kick well-saved by Halstead just before the hour-mark as chances continued to flow for Town.
All one-way, McDonald almost reduced the arrears on two occasions after cutting in from the left but the goal did eventually come on 68 minutes.
Arquin's flicked header set Olomola in on goal with the Scunthorpe loanee remaining composed to confidently find the back of the net.
Dominating proceedings since going two down Way went in search of the point his side deserved and introduced club captain Zoko for his first action since the start of August.
Continuing to pen in their opponents inside the final 10 minutes Morecambe only had their keeper to thank for retaining their lead.
Faced by two stunning 30-yard James free-kicks the Shrimps stopper produced two world-class saves to prevent a dramatic equaliser as the visitors kept coming and coming.
Into stoppage time substitute Patrick slammed a strike onto the post from the edge of the box but it wasn't to be for Town who faced the long trip back to Somerset with nothing to show for a strong performance up north.
Morecambe: Halstead; Mills, Yarney, Lavelle, Conlan; Wildig, Cranston; Mandeville (Ellison 70'), Leitch-Smith (Old 90'), Oates (Kenyon 81'); Oliver.
Bookings: Lavelle 58', Cranston 90'
Subs not used: Szcepaniak, Oswell, Hedley, Mendes-Gomes.
Yeovil Town: Baxter; James, Mugabi, Donnellan, Dickinson; Browne, Gray (Pattison 50'), D'Almeida, McDonald; Arquin (Zoko 76'), Olomola (Patrick 84').
Bookings: Olomola 10', James 15'
Subs not used: Nelson, Mahmutovic, Santos, Rogers.