All freeholders/citizens were equal under the law which by default was the British tradition (Magna Carta). Jefferson said he was not inventing something new here, simply expressing the American mind. Equality with a capital “E” and equality with a lower case “e” are two different things.
Jefferson actually believed, when he thought about it, that blacks were equal in the sense he meant–that they were entitled to self-government. It was this conviction, in tandem with his idea that a biracial society was impossible, that led him to support colonization of blacks abroad.