The incident came in the 35th minute when Mildenhall came racing out for a high ball and clashed into Mooney, who was booked by Northumberland referee Michael Oliver.
Mildenhall received treatment on the pitch for close on five minutes and then continued until half-time whereupon he was replaced by diminutive outfield substitute Craig Alcock.
While Alcock couldn't be blamed for the goals, the defence in front of him looked hesitant.
It was a disappointing first half in which neither side showed a great deal of enterprise.
Yeovil's best effort came after 28 minutes when Jaime Peters forced keeper Clayton Ince to tip the ball over for a corner.
Two minutes later came Walsall's highlight with a 20-yard shot from Edrissa Sonko being well saved by Mildenhall.
Yeovil were spirited during the second half, but Peters fired wide from a good chance set up by Liam Bridcutt in the 56th minute.
Walsall gradually took over with Sonko squandering a great 61st minute opportunity, before Lee Holmes put the home side in front after 67 minutes.
This time Sonko atoned for his previous error by setting up the pass and the on-loan winger finished neatly with a right-footed shot into the corner.
In the 77th minute Yeovil substitute Lloyd Owusu tested Ince with a high shot that the keeper caught just under the bar, but the Saddlers sewed up the points shortly before the match entered added time.
Young substitute Alex Nicholls raced clear from a header by defender Anthony Gerrard, but after Alcock parried his low shot, Kevin Betsy was on hand to provide the finishing touch.