With the use of 'for' the verb 'substituted' indicates that the subject (Player
is the substitute and therefore has been put in the place of Player A.
http://www.thefreedictionary.com/Substituted
Sub´stit´uted
a. 1. Exchanged; put in the place of another.
So it is correct by looking at what has been said so far. However I do agree it needs to be changed so something less confusing because we have a lot of players who are not native English speakers and will not understand it.
Adding an 'in' could help.
"Player B is substituted in for Player A"
or even better
"Player B is substituted in, replacing Player A"