Gestede’s towering header put the hosts ahead early in the first half before Glenn Murray tapped in a deserved equaliser just before the break.
A superb Marshall free-kick saw Blackburn regain the lead and Gestede rammed home a third as they made it five games without defeat and climbed into the top six for the first time under Gary Bowyer.
Reading have now lost five of their last six away games in all competitions and much of that was down to Marshall, who was the real architect of the win with a man-of-the-match performance that included two assists.
Reading made three changes from the win over Blackpool, including Jake Cooper who came in for the suspended Michael Hector.
Blackburn boss Gary Bowyer made one change from the win at Nottingham Forest with Gestede replacing Ryan Tunnicliffe.
The visitors should have been ahead after four minutes when Murray glanced a header onto the crossbar.
But Rovers went took the lead after 16 minutes when Marshall’s cross was met by a thumping Gestede header that sent the ball flying past Adam Federici.
The striker had an even better chance minutes later when a Jordan Rhodes shot deflected into his path six yards out but his shot was weak and straight at Federici.
But Murray gave a warning to the hosts after 18 minutes when he flashed an angled shot narrowly wide.
The best chances continued to fall to Reading, with Murray setting up Jake Taylor after 37 minutes but his well-struck shot from 20 yards was parried to safety by Jason Steele.
And they got a deserved equaliser two minutes before half-time when Jordan Obita’s wonderful teasing low cross took out the whole Blackburn defence and left Murray with a simple tap-in at the back post.
Another beauty of a cross, this time from Blackburn, almost resulted in a goal as Marshall whipped one in that Rhodes stooped to head but Federici saved initially with his leg and reacted quickly to scramble the ball clear as it trickled towards goal.
But there was no let-off for Reading after 54 minutes as Marshall curled in a wonderful free-kick from 30 yards that nestled just inside the left-hand post.
The goal meant it is the third game in the last four in which the midfielder has scored and he was instrumental in sealing the win after 67 minutes with another testing cross.
It found Rhodes in the area and although his header cannoned off the post, Gestede was on hand to slam home the rebound for his eighth of the season, ensuring Reading remain winless at Ewood Park.