The tourists resumed on 99-3 but slipped to 148-8 as five wickets fell for 15 runs, Junior Dala taking 5-34.
Ben Stokes' brisk 27 helped England to 190 all out, setting the hosts a nominal 473 to win, but they were 5-0 after two overs when the rain came.
England begin the first Test against South Africa in Durban on Boxing Day.
The visitors had dominated the first two days of this opening warm-up game, but Zambia-born seamer Dala accounted for overnight batsmen Joe Root (39) and Gary Ballance (25) who added 50 for the fourth wicket.
Keeper Jonny Bairstow was caught behind for a first-ball duck off left-armer Dieter Klein at the other end, before Moeen Ali (20) and Stokes, batting at 10, steadied the ship.
However, it was spectacular thunder and lightning which ultimately denied them the opportunity to try to bowl the hosts out and force victory.
England's final warm-up before the Tests is another three-day game against South Africa A at Pietermaritzburg, beginning on Sunday.

Court, 74, has said she would not fly on Qantas "where possible" in protest at its support of same-sex marriage.
She then told a Christian radio station "tennis is full of lesbians".
In an open letter, Navratilova said: "We should not be celebrating this kind of behaviour."
The 60-year-old addressed her letter to the Margaret Court Arena, one of the main show courts at the Australian Open.
She said: "It is now clear exactly who Court is: an amazing tennis player, and a racist and a homophobe.
"Her vitriol is not just an opinion. She is actively trying to keep LGBT people from getting equal rights (note to Court: we are human beings, too)."
In 1990, Court said Navratilova was a poor role model for young tennis players because of her homosexuality.
Navratilova said she had forgiven Court for those comments, but had only just been made aware of remarks the Australian made about South Africa's apartheid regime.
In 1970, Court said: "South Africa has the racial situation rather better organised than anyone else, certainly much better than the United States."
Court won 24 Grand Slam singles titles, 11 of them in the Open era, which began in 1968 and allowed professionals to compete alongside amateurs.
Navratilova described Court's actions as "bullying" and said sporting venues are named after athletes for "who they are as human beings" and "not just for what this person did on the field".
"The platform people like Margaret Court use needs to be made smaller, not bigger," she said.
Navratilova believes the Margaret Court Arena should be renamed after Evonne Goolagong, a 14-time Grand Slam winner of Australian Aboriginal descent.
"I think the Evonne Goolagong Arena has a great ring to it," she added. "Now there is a person we can all celebrate. On every level."
BBC Sport tennis correspondent Russell Fuller:
Freedom of speech is one thing, but Margaret Court has caused widespread offence within tennis with these most recent remarks.
Tennis Australia has so far tried to separate Court's views from her achievements as a player to argue the name of the arena does not need to change. But they will find it very hard to withstand such pressure from figures like Martina Navratilova. And the current generation of players have much influence, too.
Andy Murray, who is a member of the ATP Player Council, says it would be difficult for players to boycott a particular court during a Grand Slam. But he points out they could collectively agree a position before the tournament, which would make life very difficult indeed for Tennis Australia.
England's warm-up match against a South Africa Invitation XI was abandoned as a draw as heavy storms wrecked the third and final day in Potchefstroom.
[NEXT_CONCEPT]
Eighteen-time Grand Slam champion Martina Navratilova has renewed her call for the Margaret Court Arena to be renamed - describing the Australian as a "racist and a homophobe".