The Frenchman scored at either end of a tough, scrappy encounter that saw both teams finish the match with ten men after a pair of red cards in the final minutes.
Ambrose put City ahead midway through the first half and City looked totally in control throughout a game of few chances – even when Sevilla enjoyed extended periods of possession.
However, in a crazy last ten minutes skipper Kean Bryan received a debateable red card for foul play – which should not detract from an excellent performance from the young Mancunian, before the numbers were evened up when Eliseo was shown a second yellow.
Ambrose took advantage in stoppage time and City’s win, coupled with defeat for Juventus at the hands of Borussia Monchengladbach, means the young Blues have advanced beyond the group stage for the third successive year.
Both teams came into this encounter unbeaten on seven points, following a frustrating 1-1 draw two weeks’ ago at the Academy Stadium.
City dominated proceedings but struggled in the final third, and after being behind most of the game Sevilla levelled late to set up a crucial encounter in Spain, with both teams looking to qualify in first place and avoid a potentially tricky tie in the knockout rounds.
Patrick Vieira largely kept faith with the side that earned the point last time out, with Tosin Adarabioyo.
It was a lively start from both teams with the poor quality pitch playing a part in the succession of early chances.
City had to weather a spate of Sevilla pressure in the opening minutes, culminating in a pair of good saves from keeper Daniel Grimshaw – who did particularly well to deny Raul on 10 minutes with a low save to his right.
At the other end, Adarabioyo had City’s first effort but headed straight into the keeper’s gloves, while Kongolo was unlucky not to cap a good first half display with a goal but saw his shot blocked by the outstretched leg of a defender.
However, Sevilla’s defence was breached on the 20 minute mark with a brilliant individual goal from Ambrose, who flicked on a long ball over the top, won the resulting header and then kept his cool to fire the ball past the hand of the despairing Soriano in the Sevilla goal.
It sparked a good spell from City, who might have had a penalty when Patrick Roberts tumbled to the ground, and Bryan had the ball in the net after half an hour but Ambrose had already been penalised for a high boot.
Sevilla weren’t prepared to lie down however, and Bryan was forced to make another excellent tackle in City’s own penalty area to deny the equaliser, before Shved fired over the top after trying to do much on his own following a rapid counterattack from the hosts.
The start of the second half mirrored that of the first, with Sevilla racing out of the blocks and getting the ball in dangerous positions. Were it not for the intervention of Maffeo they would have levelled within minutes but fortunately the Spaniard got himself into the right place to make a crucial goalline block from Sanchez.
While the hosts enjoyed lots of the ball Grimshaw was rarely tested – partly due to the wayward efforts of the strikers and partly due to the resolute defending in front of him. Bryan nipped in to stem another counterattack, Sanchez had an effort blocked while Manuel miscued a free header.
At the other end, substitute Lukas Nmecha drew an excellent save from a tight angle and Maffeo fired over the bar before the antics of the closing stages were sparked by a kick in the face that sent Kean Bryan sprawling to the turf.
The altercation which followed saw Bryan see red while aggressor Raul collected a yellow card for his troubles, before Eliseo was correctly sent from the field for a poor challenge after already being booked in the first half.
It marred an entertaining game, but fortunately the final word went to Ambrose, who never stopped running all day and was justly rewarded when David Faupala unselfishly squared the ball for his compatriot to tap home in the final minute of normal time.
It was a brilliant away performance from Vieira’s young charges, who will now seek to finish the job with wins against Juve and Monchengladbach to be sure of top spot going into the next round.