The weekend's defeat for Whittingham's men set a new club record of 19 games without a win.
Pompey, with three newcomers in yet another patched-up team, held out for 63 minutes before they succumbed.
Lewis Grabban took his tally for the season to 13 with the first goal and Marc Pugh made the game safe for Bournemouth with a second after 75 minutes.
Portsmouth have now used more than 50 players with Patrick Agyemang, John Akinde and Therry Racon making their debuts.
Whittingham said: "It is like pre-season for us every week with us getting in new players. But we have to keep going because that is the situation we are in.
"The new boys did well. Agyemang and Akinde did well up front and we have some competition at last for the places up front to give the fans something to cheer about.
"I am obviously not pleased with the result, but in our position it is a big achievement just to be competitive.
"For an hour or so against the in-form team in the division I thought we did extremely well. In the first half, apart from hitting the bar, I do not think they troubled our goalkeeper.
"In the end we lost our discipline at the back. Just when we started to cause them a few problems defensively they hit us.
"There will not be any more new players. We have just created an unwanted record, but there is no alternative but to plod on."