The defeat came on a day which all four National League teams in the Wild Card standings ahead of the Marlins also lost.
"I guess [it's a blown opportunity], but at the same time, I guess it's a blessing if you're going to drop one and everyone else is too," Casey McGehee said after the Marlins fell back to a game under .500.
Hand dug the Marlins in a hole starting in the first. Charlie Blackmon led the inning off with a single to set up Nolan Arenado's two-run homer to left-center. Two batters later, Michael McKenry tacked onto that total with a solo shot.
"I gave [the Rockies] a three-run lead in the first inning and when I put my team in that situation, it's hard to come back from," Hand said.
The Marlins got two back in the second when Jeff Mathis' double brought home Adeiny Hechavarria following his one-out triple. Christian Yelich followed by singling home Mathis to complete the Marlins' first of two two-run rallies.
In the fourth, Hechavarria found himself on third again after Blackmon lost his hit in the sun. But with Mathis and Hand grounding out and Yelich striking out, the Marlins were unable to capitalize on the leadoff triple.
After erupting for 13 runs on 16 hits in series opener Friday, the Marlins totaled 23 hits over the next two games but could only produce eight runs.
"We had some more opportunities to help ourselves out and score some runs," Remond said "You've got to do that in this ballpark. ... Four runs in this ballpark is just not enough."
Hand's command issues put an end to his day in the fifth when he dished out three free passes, including one that walked in a run. After he barely missed Blackmon's head with one pitch and plunked Arenado's elbow with another, manager Mike Redmond had seen enough.
To clean up the bases-loaded mess, Redmond called on Penny, the same pitcher he picked Hand over to start Sunday's game. Penny induced a shallow fly ball and a weak grounder to keep it at a 4-2 deficit.
But with the bases loaded again the seventh, Penny couldn't repeat his magic. After Drew Stubbs' RBI double in the previous inning, DJ LeMahieu's double brought home two more to break open a three-run lead.
The Marlins' only other offensive outburst came in top of the same frame. They scored two on three consecutive hits in the seventh cut it to a 5-4 ballgame, but that's as close as Miami would get before Penny gave both runs back.
Redmond could have pinch hit-for Penny to start that inning but choose to stick with the long man to give a break to a worn-out bullpen.
"We needed some innings out of him," Redmond said. "It's wasn't perfect, but we played 13 innings [Saturday] so you've got to get as much out of guys as you can. He was our freshest arm."
In his return from a fractured glove hand that cost him over two months, Rockies right-hander Christian Bergman scattered nine hits, hanging in for 6 1/3 innings despite allowing four runs to earn his first career victory.