Palace’s early goal was the catalyst for a Bolton onslaught as Clough’s second half double sent the Whites into the lead at the County Ground.
Wanderers’ joy was short-lived as the Eagles responded through another Sekajja goal in a pulsating match where Josh Vela played 90 minutes.
After a relatively even opening to proceedings in which no opportunities arose, Sekajja broke the deadlock inside seven minutes with the first chance of the match.
Matthew Parsons latched onto a pass down the left flank before drilling in a low cross towards Sekajja, gifting the striker a glorious opportunity to side-foot the ball past Jan Ole-Sievers.
This drew a fierce reaction from Wanderers as they swiftly pushed for an equaliser.
The lively Clough tested goalkeeper David Gregory twice within the space of a minute as the Whites grew in confidence.
The frontman intercepted Quade Taylor’s header before surging towards the back-peddling defender Ryan Inniss and striking a 25-yard shot that unfortunately didn’t trouble Gregory too much.
Shortly after, Clough received possession in a similar area and was afforded a surprising amount of space as he charged towards the opposing box, allowing the striker to hit a more dangerous effort that forced the goalkeeper into glancing it wide.
Joe McKee produced an exquisite effort that was deserving of a goal when his stunning attempt came agonisingly close to levelling matters.
The Scot curled an unstoppable free-kick beyond the outstretched arm of Gregory but it rattled the underside of the crossbar. Unfortunately for Wanderers, Cian Bolger couldn’t direct the rebounding header on target under pressure as the visitors undoubtedly breathed a sigh of relief.
Bolton maintained their relentless pressure as the threatening pair of McKee and Clough came painfully close to bringing the home side back on terms.
The former powered a stinging drive from the edge of the area that Gregory palmed wide before Clough tried his luck from a similar distance - his attempt soared inches wide.
After ending the first-half undeservedly behind, Bolton made amends for their lack of luck just before the hour mark.
Jack Sampson rose to flick a pass into the path of the onrushing Clough. The pacy striker raced free of the Eagles backline before prodding the ball through the legs of Gregory to hand Bolton the equaliser they craved.
Little more than ten minutes later, Clough tormented the visitors again to reverse the scoring.
An incisive pass with the outside of Oscar Threlkeld’s foot found the youngster who quickly shifted the ball onto his right foot before firing it into the far corner.
Sadly, the Whites could only hold onto the lead for seven minutes before Parsons and Sekajja combined again to level the scoring.
On this occasion the full-back’s cross was lofted towards the unmarked striker whose header could only be pushed into the roof of the net by the stretching Ole-Sievers.
Just a minute later, the game was nearly turned on its head for a second time.
After a Palace attack, Andrew Kellet’s attempted clearance fell only as far as Connor Dymond, who was lurking on the edge of the area. The midfielder immediately reacted in almost devastating fashion as he slammed a vicious half-volley that crashed against the crossbar.
As the match neared a close, Clough came within inches of heroically stealing all three points.
An attempted shot by Sampson ricocheted back into the path of the towering frontman, allowing him to lay the ball across to Clough.
As Clough was being closed down, the striker calmly chipped a shot that boasted the required height as it flew over Gregory, but not the desired direction as it flew just wide.
BWFC: Ole-Sievers, Threlkeld, Kellett, Mills, Bolger, Vela, Lester, Gregus (Blakeman, 81), Sampson, Clough, McKee (Youngs, 75). (Unused subs: McQuade, Fielding, Maher).
CPFC: Gregory, Akuruka, Parsons, Dymond, Inniss, Taylor, Kaikai, Boateng, Sekajja, De Silva, Appiah. (Unused subs: Sow, King, Daniel, Fenwick, Gabsi).