Kyrgios produced his career highlight by knocking Rafael Nadal out of Wimbledon this summer but he was unable to dent Murray's challenge in the Canadian capital.
Murray dominated the match with his serve, producing seven aces in the two sets to book a meeting with Richard Gasquet in the next round.
The Frenchman defeated Croatia's Ivo Karlovic 5-7, 7-6 (7-5), 6-3.
It was Murray's first match since failing to defend his Wimbledon title with a last-eight exit from the All England Club last month.
Should the 27-year-old British No.1 see off Gasquet in his debut hardcourt tournament of the season - his main preparation before the US Open begins on August 25 - he could face Wimbledon champion Novak Djokovic in the quarter-finals.
"I thought I did most things pretty solidly," said Murray. The Scot lost just six service points and converted four of his five break point chances as he dismantled Kyrgios in 54 minutes.
"I didn't make too many errors," he added. "I moved well. It was a solid match for a first match back after about five weeks. I was happy."
Murray hopes his training stint in Miami with coach Amelie Mauresmo is starting to pay dividends as he aims to regain full match fitness.
"I started to feel good, actually, just before the French Open," he said. "The back felt fine throughout the grass-court season. The only problem was before that I was able to practise but not train off the court, do the stuff in the gym that makes you physically strong.
"So when I was coming up against the better players, I was just lacking a little bit. But after Wimbledon, I went over to Miami and I really trained like I used to for the first time since the surgery and I felt much better."
Djokovic, the Serbian world No.1, moved into the third round by seeing off the challenge of Frenchman Gael Monfils with a closely fought 6-2, 6-7 (4-7), 7-6 (7-2) victory.
Other men's second-round winners included 17th seed Tommy Robredo of Spain, who beat Monfils' compatriot Gilles Simon 7-5, 6-4.
Third seed Stanislas Wawrinka was given a test by French qualifier Benoit Paire, with the Swiss eventually prevailing 4-6, 6-3, 7-6 (7-2) in a contest which lasted for more than two hours.
Following Murray's win in Toronto, there was further good news for British tennis in Canada as Heather Watson edged a gruelling three-set encounter with Dominika Cibulkova to advance at the Rogers Cup in Montreal, winning 6-2, 6-7 (3-7), 7-6 (7-5). The British women's No.1 bridged a 45-place gap in the singles rankings to topple the Slovakian, who beat her in straight sets at the Australian Open earlier this year.
Watson flew out of the blocks in the opening set, with the world No.12 never even getting close to making inroads on her serve.
After that Cibulkova tightened things up and the pair were virtually inseparable as they went toe to toe in the final two sets.
But the 10th seed fell just short in the winner-takes-all final tie-break as Watson set up a third-round meeting with former world No.1 Victoria Azarenka of Belarus - seeded eight in Montreal - who beat Alize Cornet of France 6-4, 2-6, 6-4.
The toppling of another seed brought disappointment to the Montreal fans as hometown player Eugenie Bouchard was upset by American qualifier Shelby Rogers, losing 6-0, 2-6, 6-0 in their second-round match.
"I think I was feeling the pressure a little bit on the court - I felt a little match rusty, kind of," said Bouchard, who was seeded five, and was runner-up at this year's seWimbledon to Petra Kvitova. "But I knew coming into the match that I can't use those as excuses. I knew it would be kind of a difficult situation. But I'm happy I was able to at least prove to myself that I could turn things around and not let the match run away from me completely. That's definitely a positive from the match."
Joining Rogers in the next round was the world No.5, Agnieszka Radwanska of Poland, who went through with a straight-sets win over Barbora Zahlavova Strycova.
The third seed had to battle for her 6-4, 6-4 triumph though, as the Czech troubled Radwanska's serve throughout. Radwanska was broken four times during the match, but she managed to dig in and still find a way to wrap up the win in an hour and 38 minutes. Still flying the flag for the Czech Republic, however, is the No.15 seed, Lucie Safarova, a straight-sets winner over Magdalena Rybarikova of Slovakia. She triumphed 6-4, 6-2.