Despite an early lead through Jack Muldoon's fifteenth strike of the season Town conceded three first-half goals courtesy of Liam Sercombe, Sam Smith and Alfie May before Callum Wright's effort ten minutes after the break capped the win for the home side.
After securing their promotion over a week ago victory for the Robins saw them crowned as League Two champions.
Jon Stead, making a landmark 700th career appearance, was named Town captain on the day in a line-up that saw a number of changes from the one that triumphed at Wembley five days ago.
And the striker almost grabbed a goal in the opening minute when Muldoon's ball over the top played in Brendan Kiernan and his cross was deflected into his path but he couldn't get the ball under control.
Town were not to be denied though and the opening goal started and finished with Muldoon. His ball out to Mitch Roberts resulted in his deep cross being headed back by Stead into for Town's top scorer to head home.
William Hondermarck then saw his drive from the edge of the area blocked but Town were almost immediately pegged when Will Smith's slip in the wet conditions gifted May an opportunity but his effort was smartly saved by Joe Cracknell.
The open start to the game continued when the hosts did get back on level terms after 11 minutes when a speculative shot from Sercombe slipped through Cracknell's grasp.
Hondermarck's run then released Stead and his left footed strike was well hit but narrowly over Josh Griffiths's bar.
Town's defence was tested once again after 20 minutes when Matty Blair ghosted in unmarked at the far post but he headed wide of Cracknell's goal.
Stead was again involved in Town's attacking endeavours and his flick on to Kiernan saw the Town forward get in behind the defence to test Griffiths with a powerful volley.
Less than a minute later though Town were behind. A scramble in the defence saw Wright's shot pinball around the six-yard area before Smith fired home.
Ten minutes later Cheltenham added to their lead. Town failed to clear their lines following a home attack and May was on hand to poke home for his ninth of the campaign.
Kiernan then put the home side on notice that Town were not out of the game when he rattled the crossbar from 25 yards out.
On the stroke of half-time Kevin Lokko was on hand to clear the danger from a Blair cross before Cracknell was forced to be at full stretch to turn away Ben Tozer's shot from the resulting corner.
The home side were gifted a contentious free-kick in the early stages of the second-half which almost resulted in them extending their lead. A cleverly taken effort caught the Town defence off guard and Sercombe hit his effort well only for it to be deflected wide.
Town did fall 4-1 down ten minutes into the second-half when a hopeful ball forward was only half cleared and Wright made no mistake when presented with the opportunity.
Stung by the goal, Simon Weaver made four immediate changes. On came Lloyd Kerry, Josh Falkingham, Warren Burrell and Connor Hall with Hondermarck, Lokko, Roberts and Ed Francis all withdrawn.
The move helped shore up Town's shape and restricted the goalscoring opportunities for both sides with the play being largely concentrated in midfield.
With 15 minutes remaining goalscorers Smith and May were replaced by Andy Williams and George Lloyd.
Thomson's long range effort failed to test Griffiths as the final ten minutes approached, which saw Stead substituted to a standing ovation as he was replaced by Josh Andrews.
Substitute Williams almost added a fifth for the hosts before his effort was turned aside by Cracknell before the final whistle signalled the start of celebrations from the home camp.
The result saw Town finish in 17th position in what has been a memorable first season to life as an EFL club.
Cheltenham Town: Griffiths, Long, Hussey, Tozer, Raglan, Thomas, Smith (Williams, 77), May (Llloyd, 77), Blair, Wright (Azzaz, 83), Sercombe.
Subs not used: Flinders, Freestone, Chapman, Vassilev.
Goals: Sercombe (11), Smith (22), May (32), Wright (56)
Harrogate Town: Cracknell, Fallowfield, Smith, Lokko (Hall, 60), Roberts (Burrell, 60), Thomson, Francis (Falkingham, 60), Hondermarck (Kerry, 60), Stead (Roberts, 83), Muldoon, Kiernan.
Subs not used: Belshaw, Andrews.
Goal: Muldoon (7)
Referee: Benjamin Speedie.