Joao’s finish extended Blackburn’s unbeaten run under new manager Tony Mowbray to six games and moved the club out of the bottom three in the Championship.
Fulham had looked on course to claim the victory that would move them into the top six when substitute Gohi Cyriac scored his first goal for the club five minutes from time after connecting with Ruan Fredericks’ cross.
That came shortly after Craig Conway had cancelled out Sone Aluko’s 45th-minute opener when he converted from the penalty spot in the 76th minute after Tomas Kalas had brought down Marvin Emnes.
Fulham made one change to the side that beat Newcastle so emphatically on Saturday, with Fredericks returning at right-back in place of Denis Odoi.
For Blackburn, Sam Gallagher and Charlie Mulgrew both failed late fitness tests on the hamstring strains that kept them out of the weekend draw at Norwich.
Conway did return, however, having missed the trip to Carrow Road to attend the birth of his daughter and took his place on the left-hand flank in place of Liam Feeney.
Fulham’s win at Newcastle had confirmed Slavisa Jokanovic’s side as one of the form teams in the division and they immediately took the game to the visitors.
Ryan Sessegnon, the 16-year-old who scored twice on Saturday, was once again employed in an advanced position on the Fulham left and was quickly involved as the home side attempted to make their early pressure felt.
But it was striker Aluko who had the best chance in the opening exchanges, with the Cottagers’ forward unfortunate to see a close-range effort deflected wide after being set up by Tim Ream’s header.
There were more signs the visitors may be beginning to crack when centre-back Darragh Lenihan’s mistake gifted Fulham a corner and the defender was relieved to see Tom Cairney fire over the bar from the set-piece.
Jokanovic’s side had lacked a cutting edge, though, so they were relieved to see Aluko connect with Stefan Johansen’s cross on the stroke of half-time.
However, Blackburn responded well after the break and applied plenty of pressure before Conway eventually got the chance to level from the penalty spot.
Fulham appeared crushed, but responded positively when Cyriac, who has yet to start a game for the Cottagers, matched Aluko’s earlier finish.
Blackburn deserved a share of the spoils, though, and got their reward when Joao dramatically turned home Derrick Williams’ cross.