Police said the rockets had landed in open areas, without causing damage or injury. The Israeli military said they were fired from Sinai in Egypt.
Warning sirens went off just before the rockets hit. The city's airport has been closed and security tightened.
Eilat, a popular tourist destination on the Red Sea, has previously been hit by rockets fired by militants in neighbouring Egypt and Jordan.
The Egyptian military said it was investigating the incident.
Hours after the attack, a small militant Salafi group, the Mujahedeen Shura Council, said it had fired two Grad rockets at "occupied Eilat", in a statement carried on jihadist websites.
About 50,000 people live in Eilat, and tens of thousands of holidaymakers visit every year.
The Israeli military said an Iron Dome anti-rocket battery - designed to intercept short-range missiles - which was positioned near Eilat earlier this month was not deployed in the latest attack.
There were several rocket attacks on the city last year, though no injuries were caused.
Most of the rockets were fired from Sinai, which has become increasingly lawless since the revolution which toppled former Egyptian President Hosni Mubarak in 2011.
Islamic militant groups have grown in strength there and have used it as a base from which to target Israel across the lengthy shared border.

The secretary of Honeybourne Railway Club said he originally thought someone had broken into the premises, near Evesham in Worcestershire.
The floor was covered in beer and glasses and bottles smashed, Sam Boulter said.
Mr Boulter, 62, said he then saw a squirrel "staggering around" after coming out from behind a box of crisps.
He added: "There were bottles scattered around, money scattered around and he had obviously run across the bar's pumps and managed to turn on the Caffrey's tap.
"He must have flung himself on the handle and drank some as he was staggering around all over the place and moving a bit slowly.
"I've never seen a drunk squirrel before. He was sozzled and looked a bit worse for wear, shall we say."
Mr Boulter, who estimated he lost about Â£300 in the incident, eventually caught the squirrel in a waste paper bin and released it out of the window.

Just over 46,000 vehicles were registered north of the border - a year-on-year increase of more than 2.7%.
However, UK sales increased by 5.3% to almost 519,000 - the strongest month recorded since 1999.
March is typically the biggest month, accounting for about a fifth of the year's car registrations.
Last month saw Vauxhall retain its position as market leader in Scotland, with more than 10,000 units sold.
The Vauxhall Corsa remained the most popular new car, while the Ford Fiesta had a strong month and moved into the number two spot for the year to date.
The figures were compiled by the Society of Motor Manufacturers and Traders.
Top Scottish sellers in March
1. Vauxhall Corsa 2,575
2. Ford Fiesta  1,772
3. Vauxhall Astra 1,249
4. Ford Focus 1,126
5. Volkswagen Polo 1,077
Source: SMMT
Scottish Motor Trade Association chief executive Sandy Burgess said: "All areas have experienced growth with the exception of Dumfries and Galloway and Strathclyde.
"The reductions however are minimal and with the fantastic growth on 2015 numbers elsewhere, we have come out of this critical sales period well ahead for the year to date.
"We have been aware of some dealers who were experiencing new vehicle delivery issues towards the end of the month, and this may well have had a small but noticeable negative effect.
"The rest of the UK continues to show stronger growth but as we have mentioned previously this may not all be down to sales with specific manufacturers and dealers taking tactical decisions on registrations."

The midfielder more than 150 appearances for Dale before joining Tranmere in 2012, and returned for a loan spell in 2013.
The 27-year-old was released by Carlisle United at the end of the 2015-16 campaign.
Rochdale began 2016-17 with a 3-2 home defeat by Peterborough on Saturday.
Find all the latest football transfers on our dedicated page.
At least two rockets have hit the southern Israeli city of Eilat.
[NEXT_CONCEPT]
A "drunk" squirrel has caused hundreds of pounds of damage at a private members' club.
[NEXT_CONCEPT]
New car sales in Scotland grew last month but at half the rate of the UK as a whole, according to motor traders.
[NEXT_CONCEPT]
Joe Thompson has signed a six-month contract with League One side Rochdale, returning to the club with which he began his career.