The Suns missed a layup and two tip-in attempts in the closing seconds to lose for the first time in three games. Portland has won four in a row.
The Trail Blazers overcame an eight-point deficit during the final eight minutes and the lead changed hands nine times down the stretch.
A layup by Miles Plumlee with 54 seconds remaining gave Phoenix an 89-88 lead, but Lillard responded by hitting the winning shot.
Thomas Robinson scored 15 points to lead six Portland players in double figures. Robin Lopez added 13 points and 15 rebounds.
Phoenix was led by 23 points from Bledsoe and 14 from Goran Dragic.