Hume was playing the final game of his 93-day loan from Barnsley and signed off in style with a superb sidefooted finish in the 50th minute on Saturday.
The visitors had largely dominated the first half but could not make it pay and the result condemned Keane's men to a sixth successive Championship defeat.
The former Manchester United skipper was given the dreaded vote of confidence by Town chief executive Simon Clegg earlier this week.
Where this latest setback leaves him remains to be seen, but it was a badly-needed victory for Preston counterpart Darren Ferguson.
Ferguson has struggled badly this season and this was win was only North End's fifth from 21 outings so far this term.
Ferguson named an unchanged starting line-up but defender Sean St Ledger returned to the bench after missing last week's trip to Cardiff, while Ipswich were missing Gareth McAuley, Connor Wickham and Luke Hyam because of injuries.
Yet veteran Mark Kennedy returned from a hamstring problem and skipper David Norris was also passed fit to start after recovering from a virus that kept him out of last weekend's defeat by Swansea.
Preston began strongly and in the fourth minute on-loan Stoke midfielder Michael Tonge hit a right-footed shot from 30 yards which Town goalkeeper Brian Murphy saved comfortably.
Ipswich quickly gained a foothold on proceedings and midfielder Carlos Edwards had a shot blocked by Wayne Brown.
Moments later Grant Leadbitter drilled a 25-yard shot wide and striker Jason Scotland then fired a left-foot effort wide from 12 yards.
Keane's men began to build up a head of steam and in the 20th minute Rory Fallon collected possession 20 yards from goal and drilled in a fierce shot which Andy Lonergan did well to tip round a post.
In the 28th minute an inswinging corner from Danny Pugh was greeted by Billy Jones and his firm header from six yards out struck a post.
In the 30th minute, Ipswich midfielder Grant Leadbitter tried his luck from 25 yards but Lonergan was equal to his effort.
Tommy Smith then headed wide for Ipswich and Hume then blazed over the crossbar from 12 yards but he was not so wasteful five minutes after the restart.
Jones clipped a fine ball down the channel to Jon Parkin and he showed delightful footwork to cut the ball back for Hume to fire home a low right-foot finish from 12 yards.
Parkin then hit an 18-yard shot which Murphy did well to save before Tonge had a shot blocked by Kennedy as Preston went in search of a killer second goal.
Pugh twice went close with efforts from the edge of the penalty area and Darel Russell then saw an attempt blocked.
In the 68th minute, Ipswich's Troy Brown headed goalwards from 12 yards but Lonergan was again equal to the effort and saved comfortably.
Keane brought on Jaime Peters and he met a cross from Jack Colback with a firm header that Lonergan superbly tipped around a post as Preston held on.
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