The 46-year-old has been working as head of sports performance at Fratton Park since his arrival in August 2010 and will continue in that role while working alongside Whittingham.
He told the club's official website: "I've been given the title assistant manager and head of sports performance. That encompasses all medical aspects and the fitness of the players.
"It also involves identifying players for Guy who can take the club forward.
"You can see from those we've signed so far that we're mostly concentrating on players aged between 21 and 26, who also have a resale value.
"We've worked particularly hard on player recruitment since January and we've tried to get ahead of the game and sign players quickly.
"It's a real honour to hold this position and I feel proud and privileged to do it for a club of this size and stature."
Whittingham, who was confirmed as boss last month after a lengthy spell as caretaker, added: "Steve has pretty much been fulfilling the role of assistant manager since January.
"Andy Awford was a huge help on the coaching side, but Steve was doing all the off-field stuff that an assistant manager would do. I was talking to the chairman about how valuable Steve was and he replied that an assistant manager was right under my nose.
"He's the ideal man for the role of assistant manager, which he will combine with his medical duties."