Eoghan O’Connell fired an excellent winner deep into stoppage time to complete what seemed an unlikely turnaround at half time after Bryn Morris had given Pools a deserved lead with his first goal in over three years.
But the home side were on the front foot throughout the second 45 minutes and levelled through Jimmy Keohane’s close range finish before Max Clark saw a goal ruled out by referee Tom Nield soon after.
The home side weren’t to be denied though as O’Connell was allowed to advance a long way from defence to the edge of the Pools area and fire beyond Ben Killip from range as Pools suffered back-to-back defeats over the Easter weekend.
The big news of the day came hours before kick-off when Pools confirmed manager Lee would not be in the dugout at the Crown Oil Arena after testing positive for COVID-19 late on Sunday night.
And there were three changes named to a Pools side who had just five substitutes available on the bench.
Killip returned to the starting line-up having recovered from a wrist injury which kept him out of Good Friday’s defeat to Port Vale.
He replaced Huddersfield Town loanee Nicholas Bilokapic who dropped to the bench while Reagan Ogle replaced Jamie Sterry at right wing-back.
Sterry was missing after being forced off with a rib injury late in the game against Port Vale three days ago with the former Newcastle United man missing out altogether.
And in midfield, Mark Shelton was replaced by Joe White with Shelton dropping to the bench.
Despite making the trip to the Crown Oil Arena there was no place in the squad for captain Nicky Featherstone who missed out once more with a stomach injury.
But despite the disruption for Pools heading into the game they got off to the best possible start after just over 10 minutes when Morris, on-loan from Burton Albion, volleyed home in style to open the scoring, the first time in which Pools have taken the lead in the league since February 15.
Morris and White were involved in the build-up having initially hassled Corey O’Keeffe and Stephen Dooley into a mistake in midfield to force a turnover.
And White would end up on the ball over on the right where he would cut back onto his left foot and whip a delightful cross towards the back post where Morris arrived unmarked to power home a volley at the first time of asking.
Pools were playing with renewed confidence as a result of their early goal and almost doubled the lead when David Ferguson’s low cross was narrowly turned behind for a corner.
Pools did have Jake Hull to thank on the half hour though as his superb last ditch tackle prevented what looked like a certain goal from former Darlington striker Luke Charman.
Charman released Matty Done down the left and his effort deflected off Neill Byrne and looped onto Killip’s bar but fell to Charman from 12 yards, who looked destined to open his Rochdale account, only for Hull to stretch out one of those long legs to deny him.
Morris was involved again before the break when intercepting Dooley before carrying the ball some 60-yards up field beyond three Rochdale players to win a corner where he would eventually fire just over the bar from on the edge of the area as Pools went in deservedly in front at the break after an impressive showing.
But the roles were reversed after the interval with the home side dominating things in the second half with much of the game being played deep in Pools’ territory.
Clark and Done both had sighters as they fired wide of Killip’s post with Robbie Stockdale’s side pressing for an equaliser.
And try as they might, Pools could not escape their own half before the pressure told on the hour when Clark found himself in acres of space on the left and his dangerous cross was converted by Keohane who slid in at the back post for an easy finish.
Momentum was very much with Rochdale at that stage and they looked to have taken the lead moments later when a corner from the right came to Paul Downing at the back post and his cross was cleverly diverted in by Clark who wheeled away in celebration only for referee Nield to rule it out for an infringement inside a crowded penalty area.
A clash of heads involving Morris gave Pools a slight reprieve as Nelson gathered his players on the sideline.
But the message was not met his players who continued to be on the back foot as the home side pressed for a winner.
And with the game edging towards a draw, Dale found their winner in stunning style.
O’Connell picked up a loose ball midway inside his own half and was allowed to advance towards the edge of the area unchallenged before unleashing an unstoppable effort beyond Killip into the far corner as Pools were made to come away empty handed.
The result means Pools have now won just one of their last nine games as they stumble towards the end of the season with just three matches of the campaign remaining.