Armed security forces formed a tight cordon to allow the players to get on the team bus through a smoke of red flares and deafening noise from the crowd.
Angry home fans booed the players and coaches. They also threw eggs, fireworks and other objects and cried 'Bulgarian gypsies'.
"If someone was aiming to scare the team ... I can tell you it wasn't achieved," visiting coach Luboslav Penev told reporters on Thursday.
"But I don't want to comment on things unrelated to football. There are people and commissions who deal with these issues."
In September 2012 Armenia filed a protest with soccer's ruling body FIFA about "poor officiating" and the treatment they received from the home team during a 1-0 qualifying defeat in Bulgaria.
Armenia finished the Group B match in Sofia with nine men after Swiss referee Stephan Studer sent off Marcos Pinheiro in the 73rd minute and Gevord Gazaryan four minutes later.
After the match Armenian fans said they were racially abused by home supporters.
Playoff hopefuls Bulgaria, who have not reached the World Cup finals since 1998, are second with 13 points from eight matches, seven behind Italy who have already qualified for next year's finals in Brazil.
Denmark are third on 12 points followed by both Czech Republic and Armenia on nine.
(Writing by Angel Krasimirov in Sofia, editing by Tony Jimenez)
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