The Cameroon captain's injury-time spot-kick hit the crossbar, denying the four-time African champion a precious victory in its fading campaign.
Uganda beat Guinea-Bissau 2-0 to edge closer to its first Cup of Nations since 1978, when it lost in the final. Burkina Faso stayed on course for Gabon and Equatorial Guinea with a 4-1 hammering of Namibia.
Goals from Mehdi Benatia and Marouane Chamakh in the first half and Yousouff Hadji and Oussama Assaidi after the break broke open Group D for the Moroccans. All four teams had been locked on four points before the match.
On Friday, midfielder Michael Essien made his first international appearance since January 2010 as Ghana stayed unbeaten in four games with a 3-1 win over Republic of Congo.
A desperate Cameroon is five points behind Group E leader Senegal and automatic passage to the Cup of Nations with just two games to play after another disappointing result for the Indomitable Lions, who have won just one of four qualifiers. Fans protested against the team after the match and had to be dispersed by police.
Cameroon dominated in Yaounde but couldn't beat Senegal goalkeeper Bouna Coulibaly and Eto'o's late miss put one of African football's powerhouses on the brink of missing the continent's top tournament for just the second time in 30 years.
''We are in a very unfortunate position,'' said midfielder Stephane Mbia, with Cameroon now needing to win both of its final qualifiers - against Mauritius and Congo - and hope other results go its way to claim an unlikely automatic place.
It is also well off the pace in the race for one of the two best second-place spots in the 11-group qualifying competition.
Police used water cannons outside Ahmadou Ahidjo Stadium to disperse over a thousand disgruntled supporters after they prevented the Cameroon team bus from leaving the ground, blaming captain Eto'o for the team's struggles.
Uganda opened a six-point lead in Group J with goals from Godfrey Walusimbi in the 36th minute and Geoffrey Massa in the 56th at Mandela Stadium in Kampala. The Cranes are still to concede a goal in qualifying to control the group ahead of Kenya, which plays away at Angola on Sunday.
''It was a difficult match but the boys kept their composure and scored at the right time,'' Uganda's Scottish coach Bobby Williamson said.
After its hammering of the home team in Namibia, Burkina Faso needs just a point from its final match against Gambia to qualify from the three-team Group F. It's place could be sealed before that, if Gambia fails to beat the Namibians in September.
Top-ranked African team Ghana was 2-0 up through second-half goals by Isaac Vorsah and Prince Tagoe by the time Essien was substituted in his first international in 16 months on Friday.
Matt Moussilou pulled one back for the 10-men Congolese before Emmanuel Agyemang-Badu's long-range shot made it 3-1 to the 2010 African Cup finalist and World Cup quarterfinalist.
''It was a great second half performance,'' Ghana coach Goran Stevanovic said. ''I am satisfied.''
Ghana is three points clear of Sudan in Group I, having played a game more.
AP writer Emmanuel Tumanjong in Yaounde, Cameroon contributed to this report.
Gerald Imray can be reached at http://twitter.com/GeraldImrayAP