A record League Two crowd of 18,181 at Fratton Park saw Pompey, early season promotion favourites, beaten 4-1 by Oxford.
Chris Wilder's side almost got a fifth goal late on shortly after Johnny Ertl was sent off when Johnny Mullins' header came back off a post
Whittingham said: "This is a whole new team we have put together and they will take time to gel. This is only the first day and there is a long season ahead.
"For 35 minutes I thought we were doing well and looked a good team but in the end I think the emotion of the day got to us.
"The crowd were desperate for us to win and the noise they generated was unbelievable at times.
"The red card changed the game. At that stage we were 2-1 behind and we felt we could get back into the match but when Johnny went, we fell away."