The 48-year-old has been in charge of the struggling outfit as caretaker boss since November when Michael Appleton left for Blackpool.
Whittingham, who will try to spearhead a return to League One next season, has recorded just two defeats in the club's last 10 matches.
"I'd like to thank all the staff, who have worked so hard and sacrificed so much since I've been here," Whittingham told the club's official website.
"I'm also grateful to the fans for sticking with us through everything. Now we want to give them a club they can be proud of again."
New Pompey chairman Iain McInnes added: "We are delighted to have a character of Guy's calibre in charge. He understands the club and what we are trying to achieve and has shown in the past few months what he can do when he has the opportunity to work with a settled group of players."
The club, who are now being run by the Pompey Supporters' Trust, have also appointed Mark Caitlin as their new chief executive.