Fears of worsening ties came as Shiites commemorated an anniversary of the symbolic split between them and Islam's other main branch, and in the aftermath of a twin suicide bombing last week at the Iranian embassy in Beirut which was claimed by an al Qaeda-affiliated group and killed 25 people.
Bombings and shootings also continue to plague Iraq.
"The state of play is awful and it's getting worse," said Fanar Haddad, a research fellow at the National University of Singapore's Middle East Institute and author of "Sectarianism in Iraq".
"You've got the cumulative effect of 10 years of Iraq, and at the tail end of that, you've got Syria.... I shudder to think where all this is heading. It seems to be heading towards an even wider divide between Sunnis and Shiites.
"In the next few months and years, I think the worst is yet to come."
The vast majority of the world's Muslims are Sunni. But Shiites comprise a significant minority, forming the majority population in Iran, Iraq, and Bahrain with large communities elsewhere.
Although the two branches of Islam grew apart over time, their modern differences are arguably most clearly on display during the Ashura and Arbaeen commemorations, which are currently ongoing.
The ceremonies mark the anniversary of the death of Imam Hussein, a venerated figure in Shiite Islam, at the hands of the armies of the Caliph Yazid.
The recent sectarian strife is often seen as having been triggered by the 2003 US-led invasion of Iraq, which unseated Sunni dictator Saddam Hussein and left in his place Shiite-led rule.
'A widening divide'
But analysts also point to other turning points, including the 2005 assassination of Lebanon's former prime minister Rafiq Hariri and, most recently, the war in Syria.
Sunni militants in Iraq now regularly target Shiites, whom they regard as apostates, as well as the Shiite-led authorities, while in Syria, rebel groups are dominated by Sunnis opposed to the rule of President Bashar al-Assad, whose Alawite sect is an offshoot of Shiite Islam.
"Definitely, the Sunni-Shiite divide has been widening since 2005," said Sahar al-Atrache, a Lebanon analyst for the International Crisis Group, referring to the Hariri killing.
Among many Shiites, she said, there is "a kind of fear, legitimate or not", of the rise of Sunni-dominated political Islam in the region, especially on the back of the 2011 Arab Spring protests.
"This contributed to how (Lebanese Shiite movement) Hezbollah, as well as Iraq and Iran, took a sectarian position on Syria."
Syria's civil war, which in May saw Hezbollah admit it was sending fighters across the border to aid Assad's regime, has proved particularly divisive, pitting Iran and its allies against Gulf Arab countries, among others.
And the conflict, which has already claimed more than 120,000 lives since it erupted in 2011, shows no sign of easing, even with peace talks mooted for early next year.
"Sectarianism has definitely increased," said Omar Shakir, an activist from the Syrian city of Homs.
"Our regime is a sectarian regime. It forms militias that comprise fighters from one sect. And then when people see the massacres the regime commits, they react violently, in a way that is sectarian too, mirroring the hatred they received."
Meanwhile in Iraq, diplomats and officials worry that political parties -- which are largely based along sectarian and tribal lines rather than ideology -- could appeal to their base ahead of April 2014 elections, further damaging communal relations in a country that only years ago emerged from a brutal Sunni-Shiite sectarian war.
"So far all I've seen has driven towards stronger positions rather than more moderate positions," a senior Western diplomat said, speaking on condition of anonymity.
"It (the election) seems to diminish their flexibility rather than increase it.... You play to your base."