Squandered opportunities plagued the MLS entries in the semifinals. United failed to convert several times and had one strong penalty appeal denied before Pachuca substitute Damian Alvarez scored in the 76th minute.
Rod Dyachenko and Franco Niell scored to trim the aggregate margin.
Prompted by the touches of Marcelo Gallardo and Jaime Moreno and the slashing runs of Santino Quaranta, D.C. - which got more numbers in midfield by playing three in the back -- pushed Pachuca back into its own half repeatedly in a rapid-fire first half.
Luciano Emilio scuffed a volley from just six yards out on a low, driven cross, and in the final minutes of the first half Martin Cabrera uprooted him with a strong tackle as he prepared to shoot.
Keeper Zach Wells robbed Gabriel Caballero on a great scoring chance in the first half by blocking his point-blank header while scrambling across the goalmouth, and early in the second half defender Leobardo Lopez nailed a header towards the top corner that Wells soared to turn over the bar.
Minutes later, Lopez chased back into his own penalty area and grabbed Fred's jersey while knocking him to the ground but referee Jose Aguilar took no action as United players and their fans roared in disbelief.
Marc Burch replaced Quaranta and in the 60th minute swerved an excellent cross that Emilio headed sharply and keeper Miguel Calero flicked to safety.
Pachuca finally converted one of its threatening attacks to increase its edge to three goals in the 76th minute. Substitute Alvarez, who came into the match shortly before the arrival of Burch, ran onto a ball stemming from a three-pronged counterattack and thumped it past Wells.
United rallied with two deserved goals in the final minutes. Fred broke down the right flank nearly to the goal line and cut a ball back for another sub, Dyachenko, who fired it into the top corner.
Fred opened up the Pachuca defense once again when he ran onto a Gonzalo Peralta long ball and laid it into the path of Neill, whose cool finish left Calero helpless.
But Pachua held on through stoppage time to make it back to the final it won last year against Mexican rival Guadalajara.
Houston had fluffed several good chances, including a pair of free headers for Brian Ching, in the first leg at Robertson Stadium last week and went to Costa Rica tied, 0-0.
Coach Dominic Kinnear, missing several starters because of injury and suspension, had to move rookie midfielder Geoff Cameron into the back line after defender Craig Waibel aggravated a strained hamstring in the opening minutes.
He brought in midfielder Brian Mullan, himself not fully fit, and the depleted Dynamo held off Saprissa with a determined defensive effort until Armando Alonso drove a low shot that deflected off defender Pat Ianni, squirmed under keeper Tony Caig, and rolled slowly over the goal line in the 35th minute.
Celso Borges pounced on a loose ball after several attempted clearances failed and scored in the 48th minute to increase Saprissa's lead to 2-0.
The Dynamo kept battling but blew two good chances to get back in the game after the second goal.
Saprissa goalkeeper Keilor Navas fumbled a free kick from Mullan but scrambled back in time to push away a shot from Ching. Corey Ashe, not a flank factor for most of the game, drove up the left wing to drill a cross from near the corner flag that a wide-open Mullan headed yards off-target.
Jairo Arrieta added the third goal in the 77th minute when Caig rushed out of his penalty area to challenge a through ball. Arrieta got to the ball first and easily cleared the keeper to tap into the open net and leave MLS once again without a chance to capture the regional club championship.