Probably - but it's more likely he lost them and regained them later
"In the past it was often the Dark Lord's pleasure to invade the minds of his victims, creating visions designed to torture them into madness."
Severus Snape, Harry Potter and the Order of the Phoenix
Here, Severus Snape is talking about the Legilimency, a form of magic that can best be described as "mind-reading" (a term that Snape hates). From this quote, we can see that Legilimency can also be used to plant thoughts into a persons mind.
Queenie Goldstein, the woman who Jacob smiles at when she enters his bakery at the end of the film, is shown to be unusually powerful in Legilimency. Unlike Snape (himself well-practiced in the art), she is able to read minds at will and with ease.
As such, it is entirely possible that when she returned to the bakery, she "reimplanted" the memories that Jacob has lost, showing him the adventure they had been on and the time they spent together. Although most certainly illegal (the International Statute of Secrecy is taken very seriously), we're shown that she has a reason to do this - she quite clearly disagrees with the idea of Obliviating Jacob, as demonstrated by this dialogue in the film.
Jacob Kowalski: You're not going to Obliviate me?
Queenie: Of course not. You're one of us now.
It's important to note that (at least with the Obliviate spell) the effects can be reversed. In "Harry Potter and the Deathly Hallows", Hermione Granger erases her parents memories before going on the run, intending to restore them when her mission to destroy Voldemort and his Horcrux's is completed. Even if Queenie doesn't use her powerful Legilimency to return his memories to him, there is clearly other ways that the same effect could be achieved.
However, another possibility is that Jacob simply saw a beautiful woman walk into his bakery, who he was naturally attracted to, and smiled. The film makes it pretty clear that Queenie was attracted to him too - this scene could just be a hint that even without his memories fully intact, Queenie intends to form a relationship with him.