The Philadelphia 76ers today acquired Moses Malone, the National Basketball Association's most valuable player last season, in a trade with the Houston Rockets for the veteran center Caldwell Jones and Philadelphia's No. 1 selection in next year's draft.

On Sept. 2 the 76ers signed Malone to an offer sheet that reportedly would pay him a minimum of $11.8 million for six years and in excess of $15 million if several bonus clauses materialized. The Rockets, under the league rule regarding free agency, had 15 days from Sept. 2 to match that offer, or lose Malone to the 76ers.

However, on Sept. 8, the league called several provisions of the 76er offer illegal. Today, the league said from its New York office that the three most-disputed provisions had been dropped ''by mutual consent of all parties involved,'' and thus Commissioner Larry O'Brien had approved the trade.

Under the new contract, Malone, the 28-year-old center who has been the league's m.v.p. twice, still stands to make a minimum of $11.2 million. He will make an additional $100,000 in each of the next six seasons that the 76ers have a home playoff game, and another $100,000 a season if he averages 30 minutes a game, which he has done throughout his career.