Yes, he entered the new universe. But his past didn't happen to the new universe, because he didn't exist, until Amy brought him across, until that moment. "The End is the Beginning" the first trailers said, and that's literally what we have -- at the end of the series is the beginning of the Doctor's new life. Smith is the eleventh Doctor -- and the first.
Then how did someone know his phone number to call for help at the end? How did Rory remember he was the stripper at the stag party? How did River's journal fill back up? How are Torchwood and the Sarah Jane Adventures going to keep on going?
The only difference between the new universe and the old one once Amy brought the Doctor back is that everything that was eaten by the crack was no longer eaten by the crack. Or, rather, was uneaten in the same way. So rather than the crack, say, unhappening Amy's parents but Amy herself still existing despite that, now the crack unhappened, but the fish people still invaded Venice, and the Doctor still defeated the Angels at the Byzantium.
The Doctor, before Amy brought him back, was in the same sort of historical limbo the Time Lords have been in for the whole revived series. Either never heard of, or a legend, or dead if you're advanced enough to notice, but their effects on reality lingered on. And now the crack adventures are the same way. Everything's back to normal. Including the giant Cyberman and the 26 planets. So much for the idea that the cracks were going to clean up Doctor Who continuity.