The visitors, who were beaten 4-3 at leaders Al Jazira last Sunday, were dealt a blow when Henrique Luvannor was sent off in just the 10th minute in Thursday's contest.
Despite the numerical disadvantage Caio Junior's men took the lead seven minutes before the break thanks to a rare goal from defender Essa Mohammed.
However, the hosts, who are just three points above the relegation zone, were level at the break courtesy of Makhete Diop's strike.
It looked as though the match would end all square until Villanueva's late intervention, which ensured Al Shabab are just two points adrift of Al Jazira.
Second-placed Al Ain secured a comfortable 4-1 over Al Sharjah at the Hazza Bin Zayed Stadium in the other game to be played on Thursday.
Asamoah Gyan and Miroslav Stoch were among the goalscorers and Al Ain remain just one point off top spot with two games in hand.
Table-toppers Al Jazira were staring down the barrel of defeat at home to Al Wasl on Friday, after a penalty from Ederson and Caio's strike cancelled out Jucilei's sixth-minute opener.
However, Mirko Vucinic's 16th-goal in an impressive campaign sparked the comeback and further goals from Jonathan Pitroipa and Ali Ahmed Mabkhout ensured a 4-2 win.
Friday's other match saw Emirates inflict further misery on rock-bottom Al Ittihad Kalba, as they secured a 1-0 victory.
Al Fujairah triumphed 1-0 over fellow strugglers Ajman on Saturday, while champions Al Ahli were held to a goalless draw by Bani Yas and Al Wahda won 2-0 at Al Nasr.