Nelson popped up with the equaliser on 71 minutes when he met Gary Liddle's corner with a firm header from six yards out.
The visitors had looked dangerous at set-pieces all afternoon and fellow defender Sam Collins had been denied a goal in the first half when home keeper Jimmy Walker pulled off a great save.
Colchester faded in the second half, but they had been the better team before the break and they took the lead thanks to a goal from Scott Vernon in the 44th minute.
Ex-Blackpool striker Vernon only scored three goals in a stop-start season, but he was celebrating a fourth just before the break. Midfielder Anthony Wordsworth flicked on a cross by Marc Tierney and Vernon was able to control on his chest before clipping the ball past keeper Arran Lee-Barrett.
In fact, just a minute later Vernon could have doubled the lead when his goalbound shot was deflected wide of target.
Pools boss Chris Turner was adamant that his side should have been awarded a first-half penalty when striker Michael Mackay took a tumble in the box with defender Alan Maybury in close attendance, but referee Michael Jones was not convinced.
However, Pools were smiling after Nelson's equaliser and they survived a few late scares to secure a point following hot on the heels of an away win at Swindon.
Colchester's best late chance fell to substitute Stephen Gillespie, who saw his close-range shot from an angle well saved by keeper Lee-Barrett.
For Colchester, this failure to win at home has made their play-off hopes look even more remote.
They remain eight points adrift of the top six and they have some very tough away fixtures during the month of March, all of them at clubs above them in the table.