Paolo Di Canio, who resigned as Swindon manager last week, had been tipped to watch the match as a paying spectator but saw QPR play Manchester United instead.
Swindon seemed to suffer a Di Canio hangover in a lacklustre first-half display.
Town's temporary management duo of established first-team players Miller and Darren Ward picked the team and duly played in a game which saw Preston take the lead in the 51st minute through Will Hayhurst.
Swindon had to wait until the 75th minute to level when Rooney, who had only been on the pitch a matter of seconds, latched on to a poor back pass from David Buchanan to beat Rudd.
Miller said: "Making substitutions is a vital part of our job. It was a joint decision by Darren and I as to who comes on and off.
"We made the decision to bring on Adam and it paid off straight away with a goal. All season he has been in and out of the team and we know he wants to play every game."
Fellow interim player/boss Ward said: "We were disappointed not to win but there has been a lot going on at the club in the last few days so we must be happy with what we got.
"We spoke to the board on Wednesday about taking over but how long for we do not know. What we do know is that with 13 games left we have a fantastic opportunity."