Alan Anderson had 24 points, while DeMar DeRozan added 19 points for the Raptors (6-19), who hadn't won consecutive games since April 13 and 15 of last season.
Ed Davis added 13 points for Toronto.
James Harden scored 28 points for the Rockets (11-12), while Marcus Morris added 19.
The Raptors took a 77-71 lead into the fourth quarter, and stretched their advantage to nine points. But Houston made for some tense moments late in the game, cutting Toronto's lead to four points with a couple of minutes to go.
Former Raptors sharp-shooter Carlos Delfino drained two baskets in the final 1:04 to pull the Rockets to within two points, but Calderon sunk two free throws to put Toronto back up by four.
The teams traded free throws for most of the final minute. Harden, last season's Sixth Man award winner for Oklahoma City, drained a pair, Anderson went to the line to sink two, and then Chandler Parsons missed one of two with 13 seconds left.
Anderson scored on a driving reverse layup with 11 seconds to go to seal the victory for Toronto.
The Rockets have now lost seven straight on the road, a stretch that goes back to Nov. 2. It's their worst road losing streak since they dropped eight straight in 2001.
The Raptors played their third consecutive game without second-and third-leading scorers Andrea Bargnani and Kyle Lowry. Bargnani is out indefinitely with a torn ligament in his right elbow and a strained right wrist, while Lowry has a tear in his right triceps.
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Jeremy Lin, who had plenty of fans in the Air Canada Centre crowd cheering him on, was held to just seven points and two assists.
Lin was in the midst of "Linsanity" on a previous trip to Toronto last February, draining a three at the buzzer to lead the New York Knicks to a victory over the Raptors.
"If you go on anybody's career and look at it, they're going to have a period where, man, you put up ridiculous numbers," Rockets coach Kevin McHale said before the game. "I think he had one of those periods last year where everybody was, well, jeez, that's what Jeremy Lin is.
"No one in our league is a 27-point, 11-assist guy, even LeBron doesn't do that. He's figuring himself out as a young player, he really is just a young player, this is the first time he's come in and started from training camp on. Jeremy's fine, he's just going to continue to improve."
NOTES: The Rockets beat Toronto 117-101 last month. . . The Rockets wore a green stripe on their jerseys in memory of McHale's daughter Sasha, who died last month of lupus at the age of 23. Green was her favorite color. . . Raptors rookie Jonas Valanciunas was presented with the Lithuanian player of the year award from Lithuanian legend Arvydas Sabonis before tipoff. . . The Raptors are in Cleveland to face the Cavaliers on Tuesday. They return home to host Detroit on Wednesday and Orlando on Friday.
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