Canizares closed his second round Friday with three birdies in a row for his second straight 5-under 66, leaving him at 10-under.
Kaymer shot a 67. He is followed by Robert-Jan Derksen of the Netherlands, who is two shots off the lead.
Play was delayed 2½ hours because of rain and lightning.
Canizares' only European Tour victory came at the 2006 Russian Open. He lost his playing rights last season and got them back by finishing fourth at qualifying school last fall.