The Blues captain, who was returning from a four-match domestic suspension for using racist language, gave his side the lead in the 20th minute when he headed home Juan Mata’s corner to notch up his 50th Chelsea goal.
Suárez then rescued a point for Brendan Rodgers’ men when he headed home from close range in the the 73rd minute.
“We will have to wait for a scan tomorrow to understand the full extent of the injury,” said Di Matteo.
“We have just got John back after the ban and it was great seeing him lead the team out.
“He started the game very well and showed exactly his qualities, experience and influence on the team, and it was a real shame he had to go off because he was having a very good game.
“He is in pain now and we just hope it is not a serious injury and we have him back very soon.”
Di Matteo went on to express his regret at his side’s failure to build on their lead, with the west Londoners now in third place and three points behind league leaders Manchester United.
“We knew that we needed to score a second goal and it was crucial to kill the game off,” he continued.
“We had the chances to do so and their keeper made some great saves but at 1-0 it is always dangerous because the opposition can score from a set-play.”
ENHANCED ODDS: Get 2/1 on England to beat San Marino