Below are two methods. Here the function applied to the y data is Log, but any other will do as well. Also, have a look at LogLogPlot and LogLinearPlot.
xyData = RandomReal[{.1, 10}, {5, 2}]
(* {{3.7863585396010766`,2.0525620539014238`},{5.685398066640987`,4.\
020348266453116`},{7.6771838544964695`,9.879694699280535`},{4.\
361245849573017`,1.6275433819822656`},{7.313321495705271`,6.\
484234251087724`}} *)
(* mapping a pure function *)
oneWay = {#[[1]], Log[#[[2]]]} & /@ xyData
(* {{3.7863585396010766`,0.7190887952133352`},{5.685398066640987`,1.\
3913685323245182`},{7.6771838544964695`,2.290481610399797`},{4.\
361245849573017`,0.48707175034119526`},{7.313321495705271`,1.\
8693737307790999`}} *)
(* applying a rule *)
anotherWay = xyData /. {x_, y_} -> {x, Log[y]}
(* {{3.7863585396010766`,0.7190887952133352`},{5.685398066640987`,1.\
3913685323245182`},{7.6771838544964695`,2.290481610399797`},{4.\
361245849573017`,0.48707175034119526`},{7.313321495705271`,1.\
8693737307790999`}} *)