Zahi Hawass said the pyramid - of which only the base remains - is believed to be that of King Menkauhor, an obscure pharaoh who ruled for only eight years more than 4,000 years ago.
In 1842, German archaeologist Karl Richard Lepsius mentioned Menkauhor's pyramid among his finds at Saqqara, calling it the "Headless Pyramid" because its top was missing, Hawass said.
But the desert sands covered Lepsius' discovery, and no archaeologist since was able to find it.
"We have filled the gap of the missing pyramid," Hawass told reporters on a tour of the discoveries at Saqqara, the necropolis and burial site of the rulers of ancient Memphis, the capital of Egypt's Old Kingdom, south of Cairo.
Only the pyramid's base - or the superstructure as archeologists call it - was found after a 25-foot-high mound of sand was removed over the past year and a half by Hawass' team.
The base was in a 15 foot-deep pit dug out by workers, with heaps of huge rocks marking its entrance and walls. A burial chamber also was discovered.
Hawass said the style of the pyramid and of a gray granite sarcophagus lid found in the burial chamber indicates the pyramid was from the Fifth Dynasty, a period that began in 2,465 B.C. and ended in 2,325 B.C.
The period spanned approximately 140 years of the Old Kingdom. That would put it about two centuries after the completion of the Great Pyramid of Giza, believed to have been finished in 2,500 B.C.
Archaeologists have not found a cartouche - a pharaoh's name in hieroglyphs - of the pyramid's owner. But Hawass said that, based on the estimated dating of the pyramid, he was convinced it belonged to Menkauhor.
The second discovery Hawass announced Thursday was a part of a ceremonial procession road, dating back to the Ptolemaic period, which ran for about 300 years before 30 B.C.
It runs alongside Menkauhor's pyramid, leading from a mummification chamber toward the Saqqara Serapium, a network of underground tombs where sacred bulls were interred, discovered by French archaeologist August Mariette in 1850.
A high priest would carry the mummified bulls' remains down the road - the only human allegedly allowed to walk on it - to the chambers where the bulls would be placed in sarcophagi in the Serapium, about a third of a mile away, he said.
Ancient Egyptians considered Apis Bulls to be earthy incarnations of the city god of Memphis and connected with fertility and the sun-cult.
A bull would be chosen for its deep black coloring and would be required to have a single white mark between the horns. Selected by priests and honored until death, it was mummified and buried in the Serapium's underground galleries.
The sprawling archaeological site at Saqqara is most famous for the Step Pyramid of King Djoser - the oldest of Egypt's over 100 pyramids, built in the 27th century B.C.