After the first-half stalemate, more of the same followed, with Bosnia's defence blunting attacks and Swiss possession providing few opportunities.
Bosnia played aggressively, picking up two yellow cards, including one for Dzeko just after the hour mark, with the 40-year-old soon substituted.
The Swiss faced a perilous situation when, just before the hydration break, a Bosnia attack provided two clear opportunities, but the danger was seen off.
SWITZERLAND SUBSTITUTE MANZAMBI BREAKS DEADLOCK
The deadlock was broken when Manzambi scored with a right-foot shot that keeper Nikola Vasilj got a glove to but merely deflected into the net after a half-hearted defensive clearance.
Switzerland played with renewed vigour while Bosnia were rattled, their resolute defence becoming ragged.
Muharemovic was then shown a red card after 80 minutes when he charged down forward Breel Embolo just outside the box as he closed in on the Bosnia goal.
A few minutes later, a swarming Swiss attack put Bosnia in a desperate situation, with Vargas firing the ball into the bottom right corner to make it 2-0.
Their situation became almost impossible after 90 minutes when Manzambi scored again, with Vargas assisting.
Early in stoppage time Bosnia's Ermin Mahmic, who had just been brought on, scored a consolation goal with a volley from just inside the box.
Moments later Xhaka converted his penalty after Djibril Sow was fouled by Amar Memic to send the Swiss fans home beaming.
Switzerland were considered the favourites to top Group B, which also includes co-hosts Canada, but a 1-1 draw with unfancied Qatar in their opening match dented their campaign. The flurry of goals on Thursday should allay any concerns.
The stadium's 70,000 seats were a sea of Bosnia blue with scattered islands of Swiss red, revealing a crowd heavily favouring Bosnia, with a chorus of boos greeting the appearance of the Switzerland players onto the pitch and boos and whistles whenever a Swiss player moved into an attacking position.
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