The injury to Hazard overshadowed what was a positive evening for Belgium before heading off to Russia.
Romelu Lukaku was the star of the show, highlighting what a threat he will be to England when they meet in what should be a Group G decider on June 28.
The Manchester United man scored two and made one as Belgium came from behind to beat their Central American opponents, who led through Bryan Ruiz.
Dries Mertens equalised before Lukaku struck either side of half-time to take his tally to 13 goals in the last nine international games.
Lukaku also allayed any fears that Hazard's injury might be serious, telling Belgian TV: "He took a direct hit, as often. He came out as a precaution."
The Red Devils are on an 18-match unbeaten run ahead of their Group G opener with Panama next Monday.
"I think we have made progress. We did not lose, it's important. We scored a lot of goals tonight," said Lukaku.
"We will still progress before the match against Panama and we will give 120 percent against them. We will continue to make progress later."
In Austria, Senegal scored two second-half goals to beat fellow World Cup contenders South Korea 2-0 and end a four-match winless streak.
South Korea defender Kim Young-gwon deflected an effort by Alfred N'Diaye into his own goal in the 67th minute, and striker Moussa Konate added the second from the penalty spot in injury time to give Senegal their first win since beating South Africa in November.