Magus's attack on Lavos does not use the character's usual attack animation. Here is a closeup of him walloping Lavos.

Magus appears to be swinging a red weapon. This is in contrast to the white effects associated with his normal attack, as shown here:

(The video is cued up to show Magus landing a critical hit. His regular attack animation can also be seen—for example, at 2:03.)

It is also significant that this time around, Magus is fighting Lavos in Magus's own native time period—12,000 B.C., the age of Zeale—a time when dreamstone was, while not common, at least available. We do not know what wizard's plan was to defeat Lavos in 600 A.D. (except that it was going to fail), but he would certainly adjust his plans to the changed setting when he arrived back in 12,000 B.C. Magus would take advantage of all the magic that was available in that time period, most likely including dreamstone.

So, based on the appearance of the special attack animation and the setting in which this battle takes place, I think the most likely explanation is that Magus has made or otherwise obtained a dreamstone weapon (most likely a scythe) and is using that weapon to try to kill Lavos.

Magus's attack on Lavos does not use the character's usual attack animation. Here is a closeup of him walloping Lavos.

Magus appears to be swinging a red weapon. This is in contrast to the white effects associated with his normal attack, as shown here:

(The video is cued up to show Magus landing a critical hit. His regular attack animation can also be seen—for example, at 2:03.)

It is also significant that this time around, Magus is fighting Lavos in Magus's own native time period—12,000 B.C., the age of Zeale—a time when dreamstone was, while not common, at least available. We do not know what the wizard's plan was to defeat Lavos in 600 A.D. (except that it was going to fail), but he would certainly adjust his plans to the changed setting when he arrived back in 12,000 B.C. Magus would take advantage of all the magic that was available in that time period, most likely including dreamstone.

So, based on the appearance of the special attack animation and the setting in which this battle takes place, I think the most likely explanation is that Magus has made or otherwise obtained a dreamstone weapon (most likely a scythe) and is using that weapon to try to kill Lavos.