A Rembrandt etching, from 1634, and a 1504 engraving by the German artist Durer were reported missing in April.
They were found on Thursday in the library's print stacks by a conservation officer.
"We're thrilled to have found these treasures right here at home. They were found safe and sound, simply misfiled," said Library president Amy Ryan.
Durer's Adam and Eve and Rembrandt's Self-Portrait With Plumed Cap and Lowered Sabre were found in the library's storage room, following an eight-week search of 320,000 items.
Boston police, the FBI and the US attorney's office had been investigating the whereabouts of the artworks, whose combined estimated value was around $630,000 (Â£411,000), amid suggestions they had been stolen.
'Cloud lifted'
Ryan, president of the Library since 2008, announced she was stepping down earlier this week.
A damning audit - released last week - criticised the library, accusing it of ineffectual protection of special collections and disorganised storing of valuables.
The same week saw the library announce that gold coins, apparently stored in a time capsule, may have gone missing decades ago.
"It's a cloud lifted, a burden off our shoulders," Ryan told the Boston Globe, following the discovery of the missing artworks on Thursday. "Everyone is happy."
"Someone just said this to me and it's true: 'Nothing is missing under my watch'".
"All the items that we have been told are missing - but that have not been verified - went missing years before I started at BPL [Boston Public Library]."
However, Ryan insisted she would still go ahead with her resignation on 3 July despite the good news.
The Boston Public Library is the first municipally funded library in the United States and one of the first free public libraries in the world.
Two valuable artworks believed to have gone missing from Boston Public Library have been found... in the library.