Colchester went close early on when Anthony Wordsworth's fine long-range free-kick was tipped over brilliantly by Pompey goalkeeper Mikkel Andersen.
But Portsmouth went ahead on the half hour mark when Luke Rodgers latched on to Liam Walker's low defence-splitting pass and slotted calmly past goalkeeper Mark Cousins.
Freddie Sears' powerful low effort was heading in before striking Paul Connelly, but Colchester equalised in first-half stoppage-time through left-back Michael Rose's stunning first-time 30-yard strike.
Portsmouth started the second half strongly and Izale McLeod was denied by Cousins, before Liam Walker's low strike came back off the post, but Magnus Okuonghae slotted in Anthony Wordsworth's corner with six minutes to go to give the U's the lead.
But Portsmouth would not lie down and Obita tapped into an empty net after Luke Rodgers had struck the post to secure a well-deserved point.
