Spencer was stepped on during Tuesday's warm-ups for practice, and the injury cut short his practice Wednesday.
Spencer worked in individual drills Wednesday but told associate athletic trainer Britt Brown his foot was giving him a problem before team drills started.
"Happened before [Tuesday's] practice," Spencer said. "It's fine."
Cowboys officials say the injury is not deemed serious, and Spencer is listed as day-to-day.
Coach Wade Phillips said he wasn't sure if Spencer would play in Sunday's Hall of Fame Game in Canton, Ohio.
Spencer finished the 2009 season tied for third on the team in sacks (six), second in quarterback pressures (36) and tops in tackles for losses with nine.
Victor Butler, a fourth-round pick from the 2009 draft class, replaced Spencer on the first team at Wednesday's practice.
"Had a great day today," Phillips said of Butler's work in practice. "He started out slow then last four-to-five practices really practiced well and rushed the passer like we thought he could."