Rovers needed fellow promotion hopefuls Brighton and Reading to lose as well as a huge swing in goal difference to gatecrash the top six and although none of the unlikely scenarios came to pass, Blackburn fans will be encouraged for next season.
In an enthralling encounter, Tom Cairney celebrated being awarded the club's player of the year award with a fine solo goal and though Ivan Ramis equalised, Rovers struck twice more before half-time thanks to Gestede's precise finish and header.
The Latics rallied and Nicky Maynard saw a shot cleared off the line before James McClean seemingly ended Blackburn hopes with an emphatic second-half finish.
Rovers had chances to stretch the lead as Gestede rattled the woodwork and Cairney forced a fine save from Scott Carson, and they got the fourth that their play deserved through a Jordan Rhodes header.
Maynard struck late from 25 yards but Rovers deservedly held on to sign off 12 unbeaten.
Rhodes should have put Rovers ahead after 10 minutes when Josh King's low cross found him at the back post but his close range shot was blocked by Ramis.
It didn't matter because Cairney's sensational individual strike opened the scoring after 13 minutes, going past three players before slotting his sixth of the season off the post.
The lead lasted four minutes as Maynard's header hit the bar but Ramis nodded in the rebound from a yard out but Rovers quickly hit back as Conway's low cross was slotted into the bottom left corner by Gestede.
Rhodes had a header disallowed and Carson then tipped another header over from the striker, but Rovers struck again 10 minutes before the break when Conway again crossed and Gestede's towering header found the bottom right corner for his 13th of the season.
McClean flashed a shot wide and Maynard's hooked effort was cleared off the line by Grant Hanley before the end of a pulsating first half.
The second half started in a less frantic fashion but Wigan hit back when Josh McEachran's cross was not dealt with and McClean smashed home from close range.
Gestede was agonisingly close to a second Blackburn hat-trick after 64 minutes but his header rattled the woodwork and Rhodes hooked over.
Carson produced two more magnificent saves, first tipping a Cairney piledriver wide and then getting a strong hand to a low Rhodes shot.
But he was beaten again as Rhodes headed home Conway's free kick for his 25th of another prolific season six minutes from time.
Maynard's 25 yard effort arrowed into the bottom corner late on as Wigan hit back but Rovers deservedly edged it.