As did Will Chambers' try on halftime, when Melbourne received a penalty 45 seconds from the break 40m out from their own line and worked their way upfield for Waqa to skilfully knock back a Cooper Cronk kick to the Queensland winger.
Penrith opened the round-24 fixture by dominating possession and field position but Marika Koroibete opened the scoring in the 15th minute with a 95m intercept effort from a Will Smith pass.
In slippery conditions due to pre-game rain, neither side troubled the scorer again until Dallin Watene-Zelezniak crossed out wide in the 34th minute from a Matt Moylan long ball that put him outside Koroibete.
But the home side's attack struggled to find fluency against the tough Storm defence, especially on their own line, with hooker James Segeyaro absent due to the death of his father Iffysoe.
Prop Jesse Bromwich was absent due to the birth of his child.
Jamal Idris scored a deserved consolation effort in the 78th minute.
Penrith's Adam Docker was put on report for a 50th minute high shot on Tim Glasby and his teammate Jeremy Latimore copped likewise for a 57th minute 'crusher' tackle on Bryan Norrie.
Melbourne coach Craig Bellamy was impressed with the nature of the win three weeks out from the finals.
"Both sides had a lot to play for, it was pretty good performance from us," he said.
"I'm really happy with the effort."
Bellamy praised Roberts' role in the win.
"He just shows the ability he has got. I would like to see him run the ball a bit more because he is a wonderful ball carrier.
"He has certainly improved and has fitted into our structures well."
Penrith coach Ivan Cleary conceded Melbourne were superior with the ball and in defence.
"They played better at building pressure," he said.
Captain Jamie Soward added: "We created some opportunities but didn't build pressure," he said.
"We didn't finish sets and they did, they got the field possession and they scored the tries."
- AAP
