Excalibur was granted by the Lady of the Lake at Avalon.

The sword in the stone was an entirely separate sword named Clarent, and was the symbol of Arthur's sovereignty being used as a ceremonial sword. Along with the whole "Whoso pulleth out this sword of this stone is the rightwise born king of all England" stuff, Clarent would go on to be stolen and used to kill Arthur by Mordred at the Battle of Carnlann.

The story obviously varies significantly depending on the source taken, this particular one is from Historia Regum Britanniae written by Geoffry of Monmouth in the 14th century. It's one of the sources that popularised the legend so I figured this was a good one to include.

In Le Morte D'Arthur, they are different... probably.

The sword taken from the stone is not named at the time it's taken, and when Merlin takes Arthur to meet the Lady of the Lake, it's explicitly said that her sword, Excalibur, is replacing Arthur's older sword which had been broken. It might or might not have been the one from the stone... but at any rate, in Book 1, Chapter XXV, Arthur needed a sword.

And as they rode, Arthur said, I have no sword. No force, said Merlin, hereby is a sword that shall be yours, an I may. So they rode till they came to a lake, the which was a fair water and broad, and in the midst of the lake Arthur was ware of an arm clothed in white samite, that held a fair sword in that hand. Lo! said Merlin, yonder is that sword that I spake of. With that they saw a damosel going upon the lake. What damosel is that? said Arthur. That is the Lady of the Lake, said Merlin; and within that lake is a rock, and therein is as fair a place as any on earth, and richly beseen; and this damosel will come to you anon, and then speak ye fair to her that she will give you that sword.

The swords are also given different magical powers... sort of.

Excalibur (the one from the lake) is maybe probably special, but its scabbard actually protects the wearer from mortal harm. (Which is the subject of some skullduggery later in the story, when Queen Morgan Le Fay swaps out the swords and scabbards so her champion can wound Arthur.)

The sword from the stone, as Merlin reveals very soon after Arthur obtains it, has the power to blind ones enemies because it's so shiny.

But here's where we get to the hedging with the "probably." The thing is, Malory isn't really all that consistent; the sword that Arthur uses in his "first war," way back in Book 1, Chapter IX, Malory names as Excalibur:

Then he drew his sword Excalibur, but it was so bright in his enemies' eyes, that it gave light like thirty torches. And therewith he put them a-back, and slew much people.

So did he lose Excalibur and get it back? He does exactly that later on in the story... but Malory doesn't say so here. So it's kinda hard to say.

There's some more about the difference in this older discussion here.