With a tight game at Prenton Park seemingly heading for a goalless draw, the midfielder produced a moment of individual quality to clinch three points for Neil Critchley's team.
The young Reds now hold a healthy lead over nearest challengers Leicester City, with a trip to Tottenham Hotspur next up.
Derby had inflicted a first defeat of the season on the U23s back in October, and underlined their intention to complete a league double in the opening stages.
Jayden Bogle saw an effort well blocked by George Johnston inside the box early on before Kyron Stabana passed wide when he might have done better after intricate play in the hosts' area.
Returning Reds goalkeeper Danny Ward was then perhaps fortunate only to see yellow after darting out of his box and bringing down the breaking Lewis Walker.
That let-off appeared to stir the hosts, and they began to settle into a rhythm as the half wore on, creating chances as a result.
However, Toni Gomes and Ben Woodburn couldn't test the goalkeeper with their left-footed attempts from distance, while Harry Wilson's free-kick attempt was easily collected by the man between the sticks.
Liverpool lost Juanma to what appeared to be a hamstring issue just before the break, but responded by creating their best opportunity.
However, Wilson's well-struck half-volley was just about kept out by Josh Barnes, ensuring the sides went in level at half-time.
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The Reds began the second half with renewed purpose, and soon had two great chances in a matter of seconds to take the lead.
However, Gomes' initial poke was stopped by Barnes and the striker couldn't direct the follow-up anywhere but over the bar.
Derby responded by striking the bar through Luke Thomas' brilliant free-kick, but were left indebted to 'keeper Barnes immediately after when he dived at the feet of Bobby Adekanye to stop a rapid Liverpool counter providing a goal.
The Reds continued to pile the pressure on as the game progressed, but with the visitors' backline - goalkeeper Barnes in particular - holding firm, it looked like they were set for more frustration.
However, Ejaria refused to accept that outcome, taking matters into his own hands with a mazy dribble inside the box and an unstoppable finish from close range to win the game.
Liverpool U23s: Ward, Flanagan, Juanma (Lewis, 42), Jones (Masterson, 69), Johnston, Kane, Wilson, Ejaria, Gomes (Millar, 57), Woodburn, Adekanye.
Unused subs: Grabara, Jones.