Ten-man Preston looked to be heading for a precious point until Jackson cracked home a stunning shot from the edge of the box to notch an 88th minute winner.
It was only Colchester's sixth victory of the season - and their third at Layer Road.
It was also their first win in their last ten home starts.
This relegation battle was dreadful for the first 65 minutes, but the final quarter was thrilling.
It all started when Preston defender Sean St. Ledger hauled down home skipper Karl Duguid inside the box.
Referee Paul Taylor ordered a penalty and then sent off St. Ledger for a professional foul because the Preston centre-half was the last man.
Substitute Scott Vernon had only been on the pitch for seven minutes as a replacement for veteran striker Teddy Sheringham, but he took on the responsibility of converting the spot-kick to fire the U's into a 68th minute lead.
The U's had only kept one clean sheet all season - ironically in a 3-0 win at Preston way back in August - and any hopes of a second shutout were dashed when the visitors equalised in the 81st minute.
It was another goal from a substitute with ex-Liverpool striker Neil Mellor seeing his shot balloon off keeper Dean Gerken and loop into the net.
It looked as though Colchester had blown it like so many other times before this season, but on this occasion Jackson saved them with a quality late winner to give Geraint Williams' men hope of beating the drop.