The victory at Home Park on Tuesday night guided the Bluebirds to the top of the Championship.
Chopra's trio in south Devon took his tally to six goals in three Championship games this season and Jones paid tribute to the former Sunderland striker, who rejoined Cardiff in the summer.
Jones said: "I thought Chopra and (Jay) Bothroyd caused them all sorts of problems. Chops is back to his best. He looked sharp and he is a good player and as such he is difficult to contain but he's got a good foil alongside him.
"I also thought that Chris Burke and Peter Whittingham were on form but we also showed another side to us because that's a new back five, and for a 20-minute spell there in the second half we knew they we would throw everything at us and we contained them.
"We defended well when we had to and it was an all-round excellent team performance."
Chopra claimed his fourth goal of the season in the fourth minute after strike partner Bothroyd crossed from the right.
Chopra converted with a first-time strike that gave home keeper Romain Larrieu little chance.
Chopra doubled his tally in the 80th minute when he latched on to a through ball from winger Chris Burke, took a touch to go past Larrieu before firing into an unguarded net.
The striker completed his hat-trick five minutes later from the penalty spot after Burke was brought down by Argyle's Dutch defender Marcel Seip.
Chopra could have scored more. His speculative 20-yard shot crashed off the bar in the 79th minute and in the 62nd minute he raced on to a long through ball from skipper Mark Hudson but slid the ball just wide as Larrieu sped out to meet the fleet footed striker.
Argyle reduced the deficit when debutant Alan Gow converted a 90th-minute penalty after a handball by City full back Tony Capaldi, which resulted in the former Plymouth player's second yellow card and subsequent dismissal.
Argyle striker Jamie Mackie missed from eight yards in the first half and striker Rory Fallon bounced a header off the bar as Argyle swept forward with intent after the break in a bid to restore parity.
With the score still at 1-0, Argyle left back Gary Sawyer's cross-cum-shot also hit the bar.
Argyle boss Paul Sturrock said: "If Jamie had put that first half effort away, it might have been a different story. With the score going to 1-1 at half-time, it might have put a different complexion on the game but it wasn't to be.
"In the first half, our central defenders weren't with it and against players like Chopra and Bothroyd, you can't afford to give them anything. You saw what happened when we did. Cardiff are a quality team and deserved to win the game."