Through Pandoc

library(knitr)
library(kableExtra)
## LaTeX package booktabs and longtable will be loaded by default.
dt <- mtcars[1:5, 1:2]
colnames(dt)[1] <- c("mpg[note]")
rownames(dt)[2] <- c("Mazda RX4 Wag[note]")
dt[3, 2] <- paste0(dt[3, 2], "[note]")

kable(dt) %>%
  add_footnote(c("footnote 1", "footnote 2", "footnote 3"))
mpga cyl
Mazda RX4 21.0 6
Mazda RX4 Wagb 21.0 6
Datsun 710 22.8 4c
Hornet 4 Drive 21.4 6
Hornet Sportabout 18.7 8

Note: a footnote 1 b footnote 2 c footnote 3

Through HTML

Plain HTML

kable(dt, format = "html") %>%
  add_footnote(c("footnote 1", "footnote 2", "footnote 3"))
mpga cyl
Mazda RX4 21.0 6
Mazda RX4 Wagb 21.0 6
Datsun 710 22.8 4c
Hornet 4 Drive 21.4 6
Hornet Sportabout 18.7 8
a footnote 1
b footnote 2
c footnote 3

HTML + bootstrap table

kable(dt, format = "html") %>%
  kable_styling() %>%
  add_footnote(c("footnote 1", "footnote 2", "footnote 3"))
mpga cyl
Mazda RX4 21.0 6
Mazda RX4 Wagb 21.0 6
Datsun 710 22.8 4c
Hornet 4 Drive 21.4 6
Hornet Sportabout 18.7 8
a footnote 1
b footnote 2
c footnote 3