Rev Nathan Ntege, 55, walked free after a judge said immigration officers had lied on oath.
He was investigated over his work at St Jude's with St Aidan Church in Thornton Heath in South London and worshipped there on Sunday after the trial collapsed.
He was joined by the Bishop of Croydon, Rt Rev Jonathan Clark, who asked the congregation not to focus on what happened in court, but instead to focus on God.
Speaking about his return to work, the Diocese of Southwark said: "As the case has been stayed, Rev Nathan Ntege is free to return to work. The Bishop of Southwark has already met with him to discuss supervision, oversight and support in the light of the issues raised by this matter.
"The diocese takes seriously its obligation to ensure the clergy are regularly offered up-to-date advice and training in both their legal and financial responsibilities. Rev Nathan Ntege has been offered such training in the past and the diocese hopes that the renewed offer will be accepted."
During Sunday's morning service, Rev Ntege received a blessing and went on to thank parishioners for their support and prayers.
He also said he would not be doing any interviews on the matter.
The vicar was on trial last week at Inner London Crown Court on 14 counts of breaching immigration law and fraud.
However, Judge Nic Madge ruled that a number of witnesses acted unlawfully.
According to the BBC, he said: "I am satisfied that this is a case in which there has been both bad faith and serious misconduct on the part of the prosecution.
"I am satisfied that officers at the heart of this prosecution have deliberately concealed important evidence and lied on oath."
The case against six people accused alongside Mr Ntege has also collapsed.
The Crown Prosecution Service says it accepts the judge's ruling, while the Home Office says it is disappointed: "The collapse of this trial is an extremely disappointing end to a long investigation.
"We expect the highest standards from all our staff, and clearly we are treating the judge's ruling that our officers acted in bad faith with the utmost seriousness."