The experienced referee awarded Villa a spot-kick in the second half after Alan Judge was adjudged to have pulled back Villa midfielder John McGinn in the penalty area.
Striker Tammy Abraham slotted home the penalty before centre-back Tommy Elphick appeared to handle the ball as he slid in to block Colin Quaner's shot after he rounded the goalkeeper.
Former QPR manager Holloway spoke about both incidents during the match as he made it clear that referee Stroud got both decisions 'wrong'.
"It looks really soft, I must admit," Holloway told EFL on Quest on 26/01/2019. "It looks like McGinn has won that one - I think he has made a terrible mistake [referee Keith Stroud].
"That's a clear mistake [Elphick's block to deny Ipswich from scoring]. That is a blatant handball. If I am being harsh, I would say he has got them both wrong."
Abraham's penalty ended up proving to be the decisive goal because Freddy Sears' long-range effort 14 minutes from time had put the pressure back on the hosts.
After pulling a goal back, Paul Lambert's side, who failed to show any real attacking threat, did hit the post, but they didn't do enough to secure any points on the road.
As a result, Villa move within four points of sixth-placed Derby County in the table, but the Rams, who were in FA Cup action this weekend, have a game in hand.
As for Ipswich, they remain rooted to the bottom of the table and are now seven points outside of the drop zone as it is looking increasingly likely that they will be playing League One football next season.