Ipswich took the lead through Jack Colback before Brett Ormerod equalised, paving the way for Owen Garvan to score the winner 13 minutes from time.
Charlie Adam had earlier missed a disputed penalty for Blackpool, with referee Eddie Ilderton the centre of attention for that decision as well as the sendings off of Ian Evatt and Rob Edwards.
Holloway stripped off his jacket and threw it to the ground in front of the dug-out when his second player was sent off and once in the stands he shouted his disapproval at the refereeing during the match.
Holloway spent 40 minutes with the match official after the final whistle and later said: “(Ipswich manager) Roy Keane wasn’t happy with the penalty in the first-half and I wasn’t happy with the cards in the second. Why do I get sent to the stands for speaking to the officials in the same manner as Roy?
“I threw down my hat and coat because there was nothing else I could do. I let myself down but my players didn’t let me down.”
Ipswich manager Keane said: “I have got a lot of time for Ian Holloway. He is an emotional man. It is an emotional game. I did not hear him use any foul language towards the officials whatsoever.”
In the rest of the action involving non-Premier League Clubs, yesterday’s Bramall Lane clash between Sheffield United and Queens Park Rangers ended in a draw after Richard Cresswell’s goal on the stroke of half-time earned a replay for the Blades, after QPR took a 39th-minute lead through Jay Simpson.
Preston were Saturday’s big scorers as Jon Parkin’s hat-trick saw them rout Colchester 7-0.
Leicester came from behind to beat Swansea 2-1 with Dany N’Guessan bagging the 89th-minute winner.
Crystal Palace won 2-1 at Sheffield Wednesday, Neil Danns (19) and Calvin Andrew (68) scoring either side of Clint Hill’s own goal.
Graeme Dorrans (77) and substitute Chris Wood (82) earned West Brom a 2-0 win over Huddersfield and Paul Hayes scored Scunthorpe’s winner against his former club Barnsley (68).
Millwall and Derby will replay after Kris Commons’ volley (52) quickly cancelled out Lewis Grabban’s opener (49), while Plymouth and Newcastle shared a goalless draw.
Rickie Lambert’s 36th-minute free-kick saw Southampton past Blue Square Premier Luton, while Brighton beat Torquay 1-0 thanks to Andrew Crofts’ header (77).