Much was expected of the former World Cup winner's first game in charge despite a much-changed side after a disappointing World Cup for Senegal, where they went out in the last 32 after an underwhelming and error-ridden campaign.
But while Nicholas Jackson pounced on some poor defending to hand Senegal a 32nd-minute lead in Maputo, they allowed Geny Catamo to equalise for the hosts, hitting a rasping shot from outside the penalty area in first-half stoppage time.
Vieira's new-look team was without goalkeeper Edouard Mendy, who has retired, and veteran centre-back Kalidou Koulibaly, whose international career also looks at an end, plus injured Sadio Mane.
Senegal were still expected to win but came up against a highly motivated home team in an exciting tussle with chances at either end.
Also in Group J on Friday, Mohammed Mamon struck four minutes from time to hand Sudan a 1-0 win over neighbours Ethiopia.
The two former African champions were playing the match in Juba, South Sudan because of the security situation caused by the civil war in Sudan.
Guinea-Bissau opened their Group L campaign with a 2-0 win away over Tanzania in Zanzibar City with goals in either half from Franculino Dju and Mame Balde.
Tanzania are one of three co-hosts of next June's Cup of Nations finals but along with Kenya and Uganda are also participating in the qualifying competition.
The top two finishers in each of the 12 groups advance to the finals except in the groups where the hosts are playing, from which only one other team will qualify.
Friday's extensive list of qualifiers also has past winners Algeria, Egypt, Morocco, Nigeria and Zambia all in action.