In their first game back after the season was suspended because of the coronavirus pandemic in March, the reigning champions failed to find a way past the visitors, missing the chance to pull clear of second-placed FC Porto.
Although the game was played behind closed doors, some Benfica fans still gathered outside the stadium to show support to their team.
As the Benfica team bus travelled through a Lisbon motorway after the game, some perpetrators shattered the windows with stones, injuring Germany international Julian Weigl and Serbia’s Andrija Zivkovic, who were sent to hospital after being hit by broken glass.
Benfica have condemned the attack and are assisting authorities to find the perpetrators.
A club statement read: "Benfica repudiates and regrets the criminal stoning that the players' bus suffered, when it was heading to the Seixal Training Centre [Benfica's training headquarters], at the end of the game against Tondela, held on Thursday night at the Estadio da Luz.
"We inform that, as a matter of precaution, players Julian Weigl and Zivkovic were immediately taken to Hospital da Luz to be observed, following the shrapnel that hit them.
"Benfica guarantees full collaboration with the authorities, to whom it calls for the greatest effort to be made, in order to identify the offenders responsible for these criminal acts."