Born in Ty Mawr, Wales on August 8, 1846, Jones' family emigrated to New York in 1849. After a brief time in school, he started work at the age of ten. Eight years later Jones moved to Titusville, Pennsylvania, where he found work in the oil industry as a driller, pumper, tool-dresser and pipe-liner. In 1885, he moved to Lima, Ohio to take advantage of the Northwest Ohio oil boom.

In 1892 after acquiring wealth from the sale of his Lima-based Ohio Oil Company and receiving a patent on an all-metal oil sucker rod (an oil-pumping mechanism), Jones established the Acme Sucker Rod Company in an empty factory on Segur Avenue in Toledo. In addition to sucker rods, the factory produced the Acme gas engine, a dependable, single-cylinder engine powered by natural gas. An advocate of eight-hour workdays to increase employment opportunities, Jones introduced higher wages, paid vacations, and five percent bonuses. He asked his employees to work hard, to be honest, and to follow the golden rule. In return, Jones promised his employees fair wages and safe working conditions. Jones became known as Samuel "Golden Rule" Jones because of his worker policies.

In 1897, Jones received the Republican Party's nomination for mayor of Toledo. Workers united behind him after he proclaimed his "golden rule" philosophy as the platform for his administration. Jones won the election and proceeded to implement Progressive reforms. During his time in office, Jones worked to improve conditions for the working class people of Toledo. He opened free kindergartens, built parks, instituted an eight-hour day for city workers, and did much to reform the city government.

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During his first term as mayor, Jones advocated the public ownership of utilities, free parks and playgrounds, and an end to corruption in city government. He also encouraged citizens to renounce political parties since he believed non-partisan politics could unite the American people. As a result, the Republican Party refused to nominate him for a second term in 1899. Jones ran anyway and with the support of the working class, he easily won reelection, attaining 70% of the vote. He want on to serve four terms as mayor of Toledo.

Jones died in office on July 12, 1904. His successor, Brand Whitlock, continued Jones's reform efforts. His funeral was the city's largest ever. His modest gravestone is in keeping with his philosophy of the Golden Rule, inscribed on his headstone