Bird grabbed a late equaliser in last weekend's 1-1 draw at Torquay - the first professional goal of his career.
And the former non-league hot shot took his tally to three goals in two games at Fratton Park as Pompey overcame a late Exeter fightback to claim the points.
Whittingham said: "I was delighted for Ryan Bird. I know he has goals in him.
"I know from personal experience what it's like to come from non-league. He showed he's a confident player."
Bird and Patrick Agyemang both went close in the early exchanges as Pompey started the game well well in front of a bumper crowd of more than 16,000.
Exeter almost took the lead after 22 minutes as a Matt Grimes shot from 20 yards rattled the crossbar.
Pompey opened the scoring in fortuitous fashion moments before half-time when Ricky Holmes' attempted cross floated into the net.
Bird doubled the lead four minutes after the restart, planting defender Yassin Moutaouakill's centre into the bottom corner.
In-form Bird looked to have put the game out of Exeter's reach by nodding his second and Pompey's third after 71 minutes.
Danny Coles reduced the deficit with a header of his own from an Arron Davies cross four minutes later before John O'Flynn set up a nervy finish when he stabbed home the visitors' second five minutes from time.
Exeter would have snatched an unlikely point but for a brilliant save from Pompey goalkeeper Trevor Carson to deny Tom Nichols in the 88th minute.
Whittingham added: "At 3-0 we were in control but we knew they had it in them to cause us problems.
"When they pulled a goal back they had the momentum and they chucked players into the box as they had nothing to lose. I would have told our players to do exactly the same thing.
"With the ball coming in and a swirling wind something had to give but thankfully we had enough goals in the bank."