Missing his Euro 2016 contingent, Mourinho still used 22 players on his touchline debut with the Red Devils and will be content with what, in truth, was little more than a glorified training exercise.
United controlled a goalless first half before goalkeeper Jussi Jaaskelainen saw his kick charged down by Juan Mata in the 48th minute and Keane nabbed the first goal of Mourinho's reign.
Pereira found the top corner nine minutes later to secure the result, though Mourinho will surely have been more interested in bright showings from new arrivals Henrikh Mkhitaryan and Eric Bailly and England left-back Luke Shaw's first appearance in 10 months following a double leg fracture.
The DW Stadium was far from full for the Special One's bow but a sizeable contingent of United fans had made the short journey, joined by the club's executive vice-chairman Ed Woodward.
Having had disappointing experiences with David Moyes and Louis van Gaal, Woodward was present for what he will hope is the beginning of a bright new chapter.
Kick-off had to wait for the mandatory airing of 'Will Grigg's on Fire' in honour of the Latics' Northern Ireland striker, but once the whistle blew it was only a matter of seconds before Mourinho's name was bellowed from the away end.
United lined up in a 4-2-3-1 formation, with Mkhitaryan given licence to roam behind the striker.
He was quick to impress with some neat touches around the box, but Stephen Warnock went in hard and fair on Memphis Depay and Jesse Lingard to set out Wigan's stall.
United dominated a goalless 45 minutes but created just two clear chances, Mkhitaryan teeing up Memphis to poke wide before hooking over himself from 10 yards following Lingard's cross.
Wigan's best response saw Grigg lay off for Emyr Huws, whose shot was bravely blocked by Bailly.
United made seven changes at the break and two substitutes combined for the opener - Mata charging down Jaaskelainen's kick and squaring for former Wigan loanee Keane to roll into a vacant net.
Having broken the deadlock a second goal arrived in short order.
This time Ashley Young's free-kick was mis-hit by Ander Herrera and fell or Pereira, who buried his shot into the top corner from 12 yards.
Substitutions and tactical switches continued to full-time but there were no further goals.
Source : PA
Source: PA