Amazon will beat eBay this holiday season: Analyst

Amazon is likely to outperform eBay in the battle of the e-commerce giants this holiday season and beyond, Mark Mahaney, lead Internet analyst at RBC Capital Markets, said on Tuesday.

Amazon customers are less likely to see delays this year because the company has invested in developing its own delivery and logistics infrastructure, he told CNBC's "Squawk Box." Amazon got a black eye last year as consumers were left waiting for their packages.

The investment is an expensive proposition, but it allows Amazon to control the last mile of the customer experience, Mahaney said.

Read MoreRetailers weren't prepared for mobile surge

The e-commerce company is approaching the end of the distribution center and infrastructure investment cycle, he said. He believes the price-to-sales multiple is very close to a trough and the risk-reward is now attractive.

"Famous last words, but I think we're leaving the investment cycle on Amazon," he said, adding, "If we're right—and nobody's expecting this—then margins should start to recover next year and the stock goes up higher on that."

Shares of Amazon are trading at about $325. Mahaney's price target for the stock is about $420.

Following eBay's pivot back toward the consumer in the last five years, the online retailer faces structural challenges, said Mahaney.

Read More Cyber Monday wasn't as ugly as you thought

"They don't do the direct fulfillment that people expect and know from Amazon, so it's an issue when you don't get your packages right away," he said. "They also don't sell a lot of in-season retail products as well as other companies do."

Mahaney said eBay's valuation is interesting, but investors should steer clear of its stock for a while. It's too difficult at present to bet on whether another company will try to buy eBay's PayPal business, which it plans to split off into a separately traded company.

"There's one logical buyer out there. I think that's Google, but I still think the odds of that deal coming together that quickly is unlikely," he said.