df$date = as.Date(df$excel.date, format = "%d/%m/%Y")

head(df$date)
[1] NA           NA           NA           "0006-01-05" NA           NA

7/28/05
7/28/05
12/16/05
5/1/06
4/21/05

head(df$excel.date)
[1] 7/28/05  7/28/05  12/16/05 5/1/06   4/21/05  1/25/07
1079 Levels: 1/1/00 1/1/02 1/1/97 1/10/96 1/10/99 1/11/04 1/11/94 1/11/96 1/11/97 1/11/98 ... 9/9/99

str(df)
.
.
$ excel.date   : Factor w/ 1079 levels "1/1/00","1/1/02",..: 869 869 288 618 561 48 710 1022 172 241 ...

> as.Date("13/04/2014", format= "%d/%m/%Y")
[1] "2014-04-13"
> as.Date(factor("13/04/2014"), format= "%d/%m/%Y")
[1] "2014-04-13"
> as.Date(factor("13/04/14"), format= "%d/%m/%Y")
[1] "14-04-13"
> as.Date(factor("13/04/14"), format= "%d/%m/%y")
[1] "2014-04-13"

function (x, ...)  as.Date(as.character(x), ...)

x <- c("7/28/05", "7/28/05", "12/16/05", "5/1/06", "4/21/05", "1/25/07")

repairExcelDates <- function(x, yearcol=3, fmt="%m/%d/%Y") {
 x <-  do.call(rbind, lapply(strsplit(x, "/"), as.numeric))
 year <- x[,yearcol]
 if(any(year>99)) stop("dont'know what to do")
 x[,yearcol] <- ifelse(year <= as.numeric(format(Sys.Date(), "%Y")), year+2000, year + 1900)
 # if year <= current year then add 2000, otherwise add 1900
 x <- apply(x, 1, paste, collapse="/")
 as.Date(x, format=fmt)
 }

repairExcelDates(x)
# [1] "2005-07-28" "2005-07-28" "2005-12-16" "2006-05-01" "2005-04-21"
# [6] "2007-01-25"