The upmarket store scored a maximum five stars in nearly every category covered in the poll - from ease of finding products and fast-moving queues, to friendly staff and the appearance of its shops. It was only let down by a two-star score for value, and received an overall customer score of 76 per cent.
But Asda was ranked bottom in the Which? survey of more than 14,000 of its members.
The consumer group's findings suggest that shoppers like Asda's range of goods in store, but want more recyclable packaging and products without packaging, as the store received only one star for this aspect.
Which? said its findings suggest that Asda provides neither the noteworthy store experience of Waitrose or Marks & Spencer nor the value of Aldi or Lidl.
Asda scored just two stars for the quality of its own-label products.
An Asda spokesman said: "We're always happy to take feedback - but as 70 per cent of the Which? panel surveyed haven't visited an Asda in the last six months, we don't believe their findings are a true reflection of the experience of our 18 million weekly shoppers who are looking for a supermarket that provides great value, range and service to customers working to any budget.
"We are proud that our customers are recognising this, with our online grocery service growing at three times the rate of the market.
"We're constantly striving to improve our offer to our customers - be that through the efforts of our hardworking colleagues, the 1,272 new products we launched in 2019, the 530 awards we won for quality, the 8,000 tonnes of plastic packaging we removed from our stores or the 22nd annual Grocer award for being the best priced supermarket."
Bradford-based Morrisons was fifth out of the nine supermarkets surveyed with 65 per cent.
Marks & Spencer cemented its reputation for quality food and drink products, scoring five stars for both its own-brand and fresh produce.
Its overall customer score of 73 per cent placed it just below Waitrose, not managing to quite match its rival's in-store experience or product range.
Marks & Spencer was unable to match Waitrose for ease of finding products, queues or staff availability, Which? said.
Harry Rose, editor of Which? magazine, said: "The quality of fresh products is the single most important factor for our members when choosing where to shop in store, and this is just one of the areas where shoppers have told us that Waitrose excels.
"There's clear room for improvement for the 'big four' - Tesco, Sainsbury's, Morrisons and Asda - as they continue to trail behind Waitrose and M&S for experience, and behind Aldi and Lidl on value."
Aldi and Lidl were rated best for value in the Which? survey, both receiving five stars.
The two supermarkets were seen as the best for those wanting more for their money, with rock-bottom prices making customers much more forgiving of some other aspects of their shopping experience.
One Aldi customer was quoted by Which? as saying: "It's not a pleasant place to shop, but value for money is exceptional."
Sainsbury's came mid-table, with Tesco sliding in just below and Iceland coming in second-to-bottom.
Shoppers told Which? that they like Iceland's value for money, but this was not enough to boost its score overall. The supermarket received just one star for the availability of recyclable packaging.
Online supermarket Ocado, the only supermarket endorsed as a Which? "recommended provider", was not included in the analysis.
Here are supermarkets' overall customer scores, according to Which? They were rated for store appearance, product range, queues, staff availability and helpfulness, quality of own-label products, availability of recyclable packaging and value for money:
1. Waitrose, 76 per cent
2. Marks & Spencer, 73 per cent
3. Aldi, 71 per cent
4. Lidl, 67 per cent
5. Morrisons, 65 per cent
6. Sainsbury's, 64 per cent
7. Tesco, 61 per cent
8. Iceland, 60 per cent
9. Asda, 58 per cent