The Brazlian-born striker, who came on as a 58th-minute substitute, grabbed a decisive leveller with six minutes remaining to spare his side's blushes.
All eyes were on Antonio Conte's men as they looked to keep pace with Croatia at the summit of the group, and they began in style when going ahead through Yordan Minev's fourth-minute own goal.
But Bulgaria found a superb riposte, Ivelin Popov restoring parity before Iliyan Mitsanski completed the quick reversal by heading home in the 17th minute.
Such a frenetic start did not set the tone, however, as an impressive Bulgaria rearguard kept the 2006 World Champions at bay until Eder curled home with Italy staring down the prospect of a first qualifying loss for nine years.
Despite his surprise selection's crucial intervention, the result still cranks up the pressure on Conte, with his men - now two points adrift of leaders Croatia - having been far from convincing in this campaign.
Italy flew out of the blocks like a team looking to silence their critics and almost took the lead in the second minute.
Ciro Immobile got in behind the home backline, only to see an onrushing Nikolay Mihaylov keep out his effort from close range.
The goalkeeper did not cover himself in glory moments later, however, as Italy took the lead.
Mihaylov could only get a fingertip to Andrea Bertolacci's threatening cross, with the ball subsequently ricocheting off Minev and into the empty net.
Unfortunately for Conte, his men looked as susceptible at the back as their hosts.
Having been given a warning when Mihail Aleksandrov scuffed a volley after being given too much space in the area, Italy conceded a leveller.
Popov found himself unmarked 20 yards from goal and punished the visitors by unleashing a powerful shot into the bottom corner.
A second came for Bulgaria moments later - Mitsanski nodding Georgi Milanov's pin-point cross into the corner after the visitors were undone by another counter-attack.
An equaliser almost came immediately, with Immobile missing the simplest of chances when heading a Marco Verratti free-kick wide.
Italy enjoyed a spell of possessional dominance thereafter, although they were fortunate not to fall further behind when Popov's curling free-kick skimmed the bar.
The game followed a similar pattern at the beginning of the second period, only for Italy come up against a dogged Bulgaria resistance.
A chance did finally come midway through the second period, yet Immobile's effort was beaten away by Mihaylov before Bertolacci hammered the follow-up wide.
Yet his poor finishing was not replicated by Eder, with the Sampdoria striker brilliantly curling home from just outside the area.
Italy continued to press forward in search of a decisive third, but a Manolo Gabbiadini effort that snuck wide was as close as they came.
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