Freddie Ladapo scored Ipswich's 100th goal in League One this season but a double from ex-Tractor Boys youngster Jack Marriott saw Fleetwood hold the already-promoted visitors to a 2-2 draw.
The result coupled with Plymouth's victory at Port Vale ensured the West Country side denied their Suffolk rivals for the third-tier title.
Ladapo's 21st goal of the campaign gave Kieran McKenna's men a 50th-minute lead with a stunning right-foot shot which went in via the crossbar.
Ipswich, who finished the season unbeaten in 19 league games, had previously only conceded twice in 15 games.
But Marriott, having began a much-travelled career at Portman Road, breached the mean defence twice in 12 minutes to put the undefeated record in danger.
Ipswich trailed for just four minutes until substitute Marcus Harness rifled in an equaliser to beat the club's total of 100 achieved in 1960/61 under Sir Alf Ramsey.
But a frustrating afternoon saw Town reduced to 10 men for the final four minutes of stoppage time with substitute Harry Clarke booked twice in seven minutes late on.