Tykes have already signed their two permitted overseas players for the 2007 season in Australia fast bowler Jason Gillespie and Pakistan batsman Younis Khan.
However, under the controversial Kolpak ruling, Yorkshire believe Rudolph, 25, will be classed as a 'home' player and be available for selection when the English season starts in April.
"I am very proud to be a Protea and to represent my country. I will, of course, continue playing domestic cricket with the Gestetner Diamond Eagles as a Kolpak player," middle-order batsman Rudolph said in a statement Tuesday.
"This was not a decision to take lightly, and I discussed the matter fully with (national coach) Mickey Arthur and (convenor of selectors) Haroon Lorgat.
"We have all agreed with my view that this experience would be good for my cricket," the left-hander added.
In 35 Tests Rudolph has scored 2,028 runs including a best of 222 not out on debut against Bangladesh in Chittagong in 2003.
Rudolph made his decision after being overlooked by South Africa in favour of Ashwell Prince and Hashim Amla.
However, Cricket South Africa (CSA) officials believe Rudolph could yet return to international cricket following his spell at Yorkshire.
"CSA has nurtured Jacques's talent since he was a teenager, and we regard him as one of our national assets," said CSA chief executive Gerald Majola.
"However, he is only 25 and the general view is that with this added experience in county conditions he will become a more rounded player.
"We wish him all the best and are confident that he will return as an even better cricketer."
Rudolph's most recent international appearance was against Sri Lanka in August and this could yet cause a problem with his registration.
Under the rules of the England and Wales Cricket Board (ECB), to qualify as a Kolpak signing a player must not have played international cricket or first-class cricket in another country - except as an overseas player - within the 12 months prior to the start of the season.
However, Yorkshire chief executive Stewart Regan said: "The ECB have confirmed they are not able to enforce that, so as long as he has signed the declaration (not to play for South Africa) he is perfectly fine. He has given us an undertaking that he will not seek to play for South Africa while he is under contract with Yorkshire."
Rudolph's signing comes after some difficult moments in the off-season at Headingley.
Yorkshire suffered the embarrassment of seeing Chris Adams accept and then reject an offer to become their skipper and cricket chief, the former England batsman eventually opting to stay with county champions Sussex.
And home-grown ex-England batsman Anthony McGrath recently walked out of Headingley even though he had three years left on his contract and had been offered the county's captaincy after Adams's U-turn.
The Kolpak ruling was handed down by the European Court of Justice in 2004. In cricketing terms it means a player who is a national of a country which has an association agreement with the European Union, such as South Africa, and is in possession of a valid UK work permit, is treated as if he were a British or other European citizen and can therefore qualify as a domestic player for county cricket.
Yorkshire were the last English county to insist on selecting players born solely within their own boundaries, a policy that was only formally abandoned in 1992 when India's Sachin Tendulkar arrived at Headingley.
Rudolph's decision to put the county ahead of international commitments is not unprecedented.
During the mid-1970s legendary Yorkshire opening batsman Geoff Boycott opted out of England duty for three years after being overlooked for the captaincy of his country.
Yorkshire finished sixth out of nine teams in the first division of the County Championship last season, narrowly avoiding relegation.