Hughes and Melancon combined with Justin Wilson, Bryan Morris and Tony Watson for 4 1-3 scoreless relief innings.
"It's a tough spot with the bases loaded, but all I'm thinking is to keep the ball down and let my fielders make a play and that's exactly what happened," Hughes said.
Lynn allowed four runs in six innings and is winless in four starts since winning his first four starts of the season. He gave up nine hits and two walks while striking out five as the Cardinals dropped to 3-5 on their nine-game road trip.
Volquez and Jose Tabata hit consecutive run-scoring groundouts in the fourth inning before Harrison and Alvarez followed with RBI singles.
"What can I do? I gave up a bunch on infield singles," Lynn said. "It's not like I was giving up double-double-double-double. I was giving up infield singles — that's just really bad luck, and I've had those games and I've had nights when I've given up double-double-double and given up three runs.
"As a pitcher you'd much rather give up double-double-double because singles (are upsetting)."
NOTES: St. Louis C Yadier Molina, who is 0 for 12 in his last four games, got a day off. ... Pirates LHP Wandy Rodriguez will be activated from the disabled list and start Thursday at Milwaukee. He has been out with right knee inflammation since April 20. ... Cardinals LHP Jaime Garcia will make his next rehab start Monday for Triple-A Memphis on Monday after it was originally announced he would pitch for Double-A Springfield on Sunday. Garcia has been on the DL all season while recovering from shoulder surgery. ... The three-game series ends Sunday night with St. Louis RHP Shelby Miller (4-2, 3.20) facing RHP Charlie Morton (0-4, 3.45). It will mark the first time ESPN has televised a Sunday night game from Pittsburgh since 1996.