df1 <- data.frame(a=rep(1:3, each=9), b=rep(1:3, each=3), c=rep(1:9, times=3))

df2 <- do.call(rbind, lapply(split(df1, list(df1$b, df1$a)) ,
                             function(df1) df1[sample(nrow(df1), ) , ]))