Mercedes driver Hamilton and his team-mate Nico Rosberg had to take avoiding action on the slowing down lap when Alonso stopped his Ferrari in the middle of Turn 7 to give Webber a lift back to the pits.
Webber, whose Red Bull had overheated after a water leak, was reprimanded for having run on to the track before all the cars were back at parc ferme, while Alonso was also reprimanded for having created a dangerous situation.
As the incident was Webber's third reprimand of the 2013 Formula 1 season, he received a 10-place grid penalty for the next race in Korea.
Hamilton said he was surprised to have found the Ferrari stationary in the middle of the circuit, and was thankful that Webber was out of harm's way at that point.
"I was doing my in-lap, came around the corner and Fernando was there, and I was really shocked," said Hamilton.
"I went to the right of him, but if Mark had been walking across where I went then I would have run him over. Fortunately, that wasn't the case."
Despite his feelings about the specifics of this incident, Hamilton reckons that gestures like giving rivals lifts back to the pits should be allowed under the right circumstances.
"It's good for the fans to see and, as long as it's done in a safe manner - you don't stop on the racing line - then maybe it should be allowed for the future," he said.
"In sport, it's cool. Remember Nigel Mansell and Ayrton Senna [at Silverstone in 1991]. There have been times where I've driven past someone else who has stopped and I'd wished I'd stopped."