The Annunciation is a rare 19th-century copy of the altarpiece in the Cappella dell' Annunziata in Quirinal Palace, Rome, which was painted by Guido Reni in 1610.
The Transfiguration is one of many known 19th-century copies of Raphael's original, which was painted between 1518 and 1520 and hangs in the Vatican Pinacoteca.
Both pieces were donated to the Church in 1857 by Lady Clara Dry when she sold up at Quamby and returned to England after the death of her husband Sir Richard.
The couple had bought the paintings on their honeymoon to Italy in the mid-19th century and had them framed in London.
Bishop Phillip Newell dedicated the paintings at a special ceremony yesterday.
The museum's painting conservator Mar Gomez said that the restoration of the paintings had begun in May and finished just a week ago.
"They were not in bad condition but mainly dirty," she said.
"The frames were quite damaged; we had to replace many missing parts."
Minister the Rev. Ken Box said that The Transfiguration was the 15th-century equivalent of a Power Point presentation of the Gospel.
"It tells the story from start to finish," he said.
"The ministers would have preached from the painting."
Church warden Margaret Bramich, who has attended St Mary's for 53 years, said that the paintings made the church complete.
"When they were down, everyone missed them," she said.