Southampton had an early goal overturned for offside following a VAR review but went ahead on 20 minutes when Ward-Prowse’s cross was headed in by Jannik Vestergaard.
Ward-Prowse then netted from two superb set-pieces on a 26th birthday to remember for the Southampton captain.
In the second half Danny Ings crashed in a fourth Saints goal off the crossbar before the striker was forced off injured.
Tyrone Mings pulled one back for Villa from Jack Grealish's cross and the hosts set up a nervy finish with two goals in stoppage time.
Ollie Watkins converted a penalty won by Grealish who then caught Alex McCarthy unsighted from long range.
But Southampton held on to make their best start after seven matches since 2014/15. Villa drop to sixth after back-to-back defeats.
Budweiser King of the Match: Jack Grealish (AVL)
Aston Villa: 8 Nov v Arsenal (A)
Southampton: 6 Nov v Newcastle (H)