Agbayani, who was eligible for salary arbitration, will make $600,000 in 2002 and can earn an additional $350,000 in incentives based on plate appearances.
The Hawaiian native, who turns 30 on Dec. 28, played in only 91 games during an injury-plagued 2001 season, batting .277 with six homers and 27 RBI.
Agbayani was on the disabled list from April 9-25 with a chip fracture in his left wrist. He also fractured a bone in his right hand while swinging against Florida on Sept. 1 and missed the rest of the season.
Johnson, 35, led all major leaguers in pinch hits last season, going 11-for-27 (.407) off the bench. Overall, he batted .254 with six homers and 23 RBI in 64 contests for the Mets.
Jones, 29, spent the entire 2001 campaign on the disabled list with a variety of injuries. He began the year on the DL with tendinitis, then strained his right knee during a rehabilitation assignment at Class A St. Lucie on May 26.
Johnson and Jones received an invitation to spring training.