Alonso was catching Lance Stroll for sixth but opted not to risk damage to his or his team-mate's car, and stayed behind in seventh until the chequered flag.
Aston remained ahead of Ferrari in the standings, as only Carlos Sainz could reach the top 10 due to Charles Leclerc's woeful lack of pace all weekend.
“They [Mercedes] are fast. They are a concern for us,” Alonso told Sky Sports.
“They have been all year long. They have very consistent drivers as well. Ferrari is a very fast car, but they seem to score only with one car or have more trouble in the race.
“But the Mercedes is always there. It’s going to be a very tough competitor. We didn’t have the pace. We were not fast enough with the soft, not quick enough on the hards at the end.
“So, I don’t think it was a thing on the strategy or anything, it was just a lack of pace today. Let’s see why and try to get better for Canada.”