The Eagles swept the Towers 3-0 in regular league games, just like last season, but could not get past them to reach the semi-finals at Wembley over the first weekend of May.
Towers trailed after the first game in the best of three series, but Randy Duck topped their scorers again on Saturday with 24 points, after leading them to victory on Thursday to square the series.
The Towers, who moved most of their games to Crystal Palace this season, return to their original Wembley home for the play-off finals, where they will face league champions Sheffield Sharks in the first semi-final.
Manchester Giants will play Thames Valley Tigers in the second semi, after beating last season's play-off winners Birmingham Bullets 90-77 on Saturday. The Sharks beat Great London Leopards 75-68 on Friday to win their series 2-1.
Tigers earlier eliminated Derby Storm 2-0 and were the only team to win an away game in the quarter-finals, as the top quartet in the league qualified for Wembley.
Tony Dorsey, who led Birmingham to the play-off title last season, scored 34 points for Giants against the Bullets on Saturday as Manchester pulled away in the fourth quarter.