Another embarrassing exit for English football at a major tournament was looming in Gelsenkirchen until Bellingham's acrobatic effort in the 95th minute broke Slovak hearts.
A minute into extra-time, Harry Kane then completed the comeback to set up a meeting with Switzerland on Saturday in the quarter-finals.
However, any excitement among the England fan base at ending up on the perceived weaker side of the draw was drained away by another turgid performance from Gareth Southgate's men.
England arrived in Germany hyped as pre-tournament favourites thanks to a squad stacked with attacking talent.
Slovakia coach Francesco Calzona insisted on the eve of the game that Southgate is working with "the best squad at the Euros".
But a team featuring the Bundesliga's top scorer Kane, the Premier League's player of the year Phil Foden and a recently crowned Champions League winner in Bellingham has been laboured in possession and easy to defend against.
Until Bellingham's late intervention, England had scored just two goals in four games, while the deficiencies of a makeshift back line were also exploited by Slovakia early on.
The side ranked 45th in the world had already spurned two big chances before Ivan Schranz strolled through the heart of the England defence to slot home his third goal of the tournament on 25 minutes.
England fans dominated all but a small section of the 50,000 capacity AufSchalke Arena and made their disillusionment heard as boos greeted the half-time whistle.
Southgate's men marginally improved after the break but bar a header Kane sent wide from a free-kick and a Declan Rice shot from distance that came back off the post, they had created little as Slovakia sat deep to defend their lead.
After a 0-0 draw against Slovenia that had guaranteed top spot in Group C, Southgate had bemoaned an "unusual atmosphere" as he was pelted with empty beer cups by disgruntled supporters.
'Scoring goals is my release'
The England manager and his players were braced for an even more severe outpouring of rage until Bellingham produced a moment of brilliance that allowed him to answer his critics after two underwhelming performances against Denmark and Slovenia.
"Playing for England, it's a lot of pleasure but you also hear a lot of people talk a lot of rubbish. It's nice when you deliver you can give them a little bit back," said the Real Madrid star of his goal celebration.
"For me playing football, being on the pitch, scoring goals is my release and it's maybe a message to a few people."
Southgate was more understanding of the wave of criticism that is still set to come his side's way before they face the Swiss in Duesseldorf.
"We're putting a plaster over things and giving young players opportunities," said Southgate.
"We're somehow finding a way. I can imagine how everyone is going to react even though we've won but we are still in there. The one thing that cannot be questioned is the desire, the commitment, the character."
The spotlight is on Southgate to find a solution over the next six days to avoid failing again to deliver major tournament glory at his fourth attempt.
Switzerland made light work of beating holders Italy 2-0 on Saturday and are a significant step-up in quality from Slovakia.
The England boss hailed the impact of his substitutes.
Eberechi Eze and Ivan Toney played a part in Kane's winning goal, while Cole Palmer added some thrust from midfield.
However, the fact it took 66 minutes for Southgate to make any changes and his stubbornness in starting 10 of the same 11 in all four games so far has left his judgement open to question.
Bellingham's intervention ensures Southgate will take charge of his country for the 100th time in the quarter-finals.
But England will need to be much improved if he is to stay in his job beyond the century mark.
