Ipswich condemned Hull to the Championship play-offs - but the Suffolk side's 1-0 victory was not enough to propel them into the top six.
An inspired substitution from boss Jim Magilton won the game for the home side after Alan Lee scored a minute after coming off the bench.
Lee headed into the bottom corner in the 70th minute after being set up by former Hull striker Jonathan Walters.
The defeat means the Tigers miss out on the chance of immediate promotion to the top flight for the first time in their history.
They will now face the lottery of the play-offs, while Ipswich are resigned to another season in the Championship.
In a nervy clash played in sweltering conditions, Ipswich had the better opportunities and could have won by a greater margin but Pablo Counago and Tommy Miller were both denied by the woodwork in the first half.