The Eagles led 3-1 after the first leg and went further ahead in the 25th minute at a crackling Selhurst Park, courtesy of an own goal from Pedro Henrique.
Eguinaldo levelled later in the first half but Ismaila Sarr continued his rich vein of form by scoring his ninth goal of the competition early in the second period to make it 2-1 on the night.
Glasner’s men will face Rayo Vallecano in the final in Leipzig later this month after the Spanish side beat Strasbourg 2-0 on aggregate.
Palace had the ball in the net within the first 10 minutes, against the run of play, only for Yeremy Pino’s goal to be ruled out for a marginal offside.
But the home side extended their aggregate lead 15 minutes later after a surging attack, with Adam Wharton at the centre of the move.
Dmytro Riznyk palmed away Wharton’s stinging long-range shot but was helpless as Daniel Munoz’s follow-up from a tight angle flicked off Henrique and flew past him.
Eguinaldo made it 1-1 in the second leg for the exiled Ukrainian team with a nonchalant finish into the top corner, leaving Palace goalkeeper Dean Henderson rooted to the spot.
Jean-Philippe Mateta crashed a shot against the post with an audacious scissor-kick shortly before half-time as the home side continued to threaten.
The tie was effectively over soon after the restart when Sarr turned in Tyrick Mitchell’s cross from close range and Palace saw out the game comfortably.
The final in Leipzig on May 27 will be Glasner’s final match in charge after he announced earlier this season that he would leave when his contract expires next month.
The 51-year-old Austrian, who arrived early in 2024, has overseen a golden period for Palace, guiding them to a 1-0 win over Manchester City in last season’s FA Cup final – the club’s first major trophy.
Palace then beat Liverpool on penalties in the season-opening Community Shield.
Europe’s third-tier competition was only launched in 2021 and two of the four winners so far have been London clubs – West Ham in 2023 and Chelsea last season.
Palace are only in the competition because they were demoted from the Europa League before the start of the season after Uefa ruled they had breached multi-club ownership rules.
Winning the Conference League would guarantee entry into next season’s Europa League.
Glasner, who won the Europa League with Eintracht Frankfurt in 2022, was in sparkling form in his pre-match press conference on Wednesday, saying his players wanted to taste the “honey” again after winning the FA Cup last year.
Now they have the chance of a sweetest end to their season. (AFP)