The two dramatists will now jointly appear on the title pages for the Henry VI plays in New Oxford Shakespeare.
Researchers have verified Marlowe`s contribution "strongly and clearly enough", editor Gary Taylor said.
Marlowe, who is known for writing plays including Doctor Faustus, was first suspected of contributing to Henry VI Parts I, II and III - along with other Shakespeare plays - as far back as the 18th Century.
But this marks the first time he has received an official credit.
`Rivals sometimes collaborate`
Scholars working on New Oxford Shakespeare, a collection of all of Shakespeare`s known works, said his collaboration with other playwrights was more extensive than has previously been known.
The research, by 23 international scholars, has identified 17 of 44 Shakespeare plays as being co-written with other authors.
The new research involved both traditional textual analysis and the use of computerised tools to examine the scripts.
Gary Taylor, one of the New Oxford Shakespeare`s general editors, told The Guardian: "We have been able to verify Marlowe`s presence in those three plays strongly and clearly enough.
"We can now be confident that they didn`t just influence each other, but they worked with each other. Rivals sometimes collaborate."
Carol Rutter, professor of Shakespeare and performance studies at the University of Warwick, told BBC News: "It will still be open for people to make up their own minds. I don`t think [Oxford University Press] putting their brand mark on an attribution settles the issue for most people."
But it is clear Shakespeare did work with several other figures in theatre at the time, she added.
"I believe Shakespeare collaborated with all kinds of people... but I would be very surprised if Marlowe was one of them," she said.
Asked who else might have influenced Shakespeare`s work, Prof Rutter said: "I would suggest we should look not to another playwright but to the actors.
"Yes, Shakespeare collaborated. But it`s much more likely that he started his career working for a company where he was already an actor, and collaborated not with another playwright but with the actors - who will have had Marlowe very much in their heads, on the stage, in their voices.
"They were the ones putting Marlowe`s influence into the plays."
Prof Rutter added: "We have really stopped thinking about the richness of the writing experience in the early modern theatre, and by crediting Marlowe, people like Gary Taylor are making us attend to that."
The authorship of Shakespeare`s works have been debated for centuries. Academics have suggested that four writers - including Marlowe - wrote some or all of his plays.
The film Anonymous, released in 2011, suggested Edward de Vere, 17th Earl of Oxford, was behind the playwright`s works.
Actor Mark Rylance, who appeared in the film, also chairs the Shakespearean Authorship Trust, the society which has argued since 1922 that the writer was unlikely to be the true author of the plays credited to him.
Other playwrights put forward as being the real authors include Sir Francis Bacon and William Stanley, 6th Earl of Derby.
High-profile figures who have voiced doubts about Shakespeare being the true author include Charlie Chaplin and Mark Twain, who said: "So far as anybody actually knows and can prove, Shakespeare of Stratford-on-Avon never wrote a play in his life."
