The spot kick came five minutes after the Gills had seemingly completed a comeback from a goal down to lead 2-1 through goals from John Marquis and sub Luke Norris. This after Gozie Ugwu had given the Glovers a 21st minute lead with his fourth goal of the season.
The result leaves Yeovil rooted to the foot of the table and now five points from safety after the other results went against them but a second successive comeback at home
will give Terry Skiverton's side hope that they can complete "Mission Survival".
With four new players arriving at Huish Park, three of them found their way into the starting eleven. Swansea loanee Stephen KIngsley came in at wing back along with team mate Josh Sheehan in midfield and the return of Millwall's centre back Byron Webster on loan. Dropping to the bench was Kieffer Moore with Ben Nugent and Ajay Leitch-Smith missing from the squad altogether.
The first twenty minutes were very quiet and lacked any chances at all, the only incident seeing Nathan Smith booked for a foul on John Marquis on eleven minutes. But the opener was just around the corner and it arrived on 21 minutes. Sam Foley's free kick was partly cleared to Webster who nodded the ball forward back into the box. Gozie Ugwu controlled the ball and fired home as the Gills defence appealed in vain for offside.
Within two minutes, Yeovil had a double golden chance to make the score 2-0. James Berrett robbed Max Ehmer and released Ugwu down the right; the striker crossed for James Hayter whose first shot was saved by keeper Stuart Nelson with the follow up blocked for a corner.
Gillingham, unbeaten in seven, were being kept at arms length by the Glovers back line and it took 35 minutes for the away side to create a clear chance, Cody McDonald wasting a headed opportunity. Ugwu was sent clear right late in the half but lifted his shot over Nelson and wide of the post.
Gills new boss Justin Edinburgh got into his lacklustre side at half time and they came out much improved and equalised three minutes after the break. McDonald's free kick was well saved by keeper Artur Krysiak but Marquis followed up to strike his sixth goal in eight games.
Sheehan was impressive all afternoon in Yeovil's engine room and he twice had attempts on goal in a couple of minutes midway through the half, neither really testing Nelson. Foley then forced Nelson into a flying save with a swerving effort from 25 yards out on 78 minutes.
Skiverton sent on Adam Morgan for Berrett with twelve minutes left and the lively striker almost produced a sensational goal when he collected Krysiak's throw deep in his own half, ran sixty yards before unleashing a shot that went high and wide.
With three minutes left, Gills looked to have sealed a win they possibly didn't deserve when sub Luke Norris, only on for five minutes, was allowed time and space to send in a shot into the far corner of Krysiak's net.
But this Yeovil side had come back from a goal down to win at Crawley a fortnight ago and they showed a similar battling spirit again, refusing to give in. Nathan Smith's looping cross wasn't dealt with by the Gills defence and Joel Grant won the ball before going down under the challenge of a Gills defender. Ref Simon Hooper pointed to the spot and, showing great guts and determination, Morgan smashed the penalty home to grab a deserved point for the Glovers.
Visiting centre back John Egan headed a corner over five minutes into stoppage time but Yeovil held on to gain a point and make it four home games unbeaten.