How can I rename all columns of a data frame based on another data frame in R?

A    B    C   D
1    2    3   4

DataFrame1 <- read.table(con <- file("clipboard"), header=T)

Col1    Col2
A       E
B       Q
C       R
D       Z

DataFrame2 <- read.table(con <- file("clipboard"), header=T)

colnames(DataFrame1) <- DataFrame2$Col2

If the column names didn't go in order like they do in the example you'd have to use match:

DataFrame2$Col2[match(names(DataFrame1),DataFrame2$Col1)]