The memorial has a teddy bear looking over the top and features a verse in Welsh about a small, pink star.
Five-year-old April was abducted and killed by Mark Bridger, 47, of Ceinws, Powys, in a sexually motivated attack in October 2012.
He was jailed for life in May 2013.
Visiting the grave, April's mother, Coral Jones, 42, said: "It's April down to a tee. She loved her teddies and was fascinated by butterflies and shooting stars.
"We've been waiting two years for this day. It's lovely that the headstone will be in place for Christmas and we plan to visit her on Christmas Day."
April's father, Paul Jones, 46, added: "It's horrible seeing our daughter's name on a cold stone in a graveyard but this is a really lovely tribute to her."
April's body was never found despite the biggest search in UK police history.
Bridger was handed a rare whole life jail term after fragments of her skull were found in his fireplace.
Her funeral was held in September 2013 and she was buried in a graveyard just yards from where she was last seen alive.
Her mother added: "Even though we had the funeral last year, we had to wait for the ground around April's grave to settle before we could put the headstone up.
"It's a massive relief now it's finally here as before we just had a little tag with her name on it. It's much more personal."
A headstone marking the grave of murdered schoolgirl April Jones has been put in place more than two years after she was killed.