The 18th-placed Latics, who would have moved out of the Barclays Premier League relegation zone had they hung on for all three points, instead had to settle for a 2-2 draw with Spurs at the DW Stadium after the ball bobbled off the unfortunate Emmerson Boyce into his own net in the 90th minute.
It had hit Boyce from a Tom Huddlestone free-kick that resulted from a coming-together between Spurs full-back Kyle Walker and his opposite number Jean Beausejour.
Martinez felt the match officials made an incorrect call over the incident, saying after the game: "If you see the replays, it puts extra salt in the wounds.
"It was not a free-kick - it should never have been a free-kick.
"Kyle Walker is pulling Jean Beausejour and he is too honest, staying on his feet.
"We need to accept that - sometimes when you are down there, the results or the lucky breaks don't go your way."
Despite his disappointment at the way it finished, Martinez was keen to praise his players' efforts during a contest in which an early defensive blunder by the hosts had allowed Champions League-chasing Tottenham to open the scoring.
A hesitant exchange of passes between Latics defender Maynor Figueroa and goalkeeper Joel Robles in the ninth minute led to the latter cannoning an attempted clearance against the outstretched leg of the approaching Gareth Bale, and the ball rebounded straight into the net.
Wigan equalised within two minutes through a header from Boyce, whose late own-goal subsequently cancelled out the Callum McManaman thunderbolt had made put them 2-1 up four minutes into the second half.
Martinez's side are now two points adrift of 17th-placed Aston Villa, their opponents at the DW Stadium on the final day of the season, with both teams having three other games to play first.
Reflecting on the match, he said: "We made the worst possible start against a side that was focused and wanted to win.
"We gave them a goal lead, but from that point on I thought we were magnificent.
"It is just unfortunate that Spurs had the opportunity to put a lot of pressure on us from that dead-ball situation, which I think is a little bit unfair - if you limit Spurs to so little from open play, you should get a little bit more luck."
Martinez added: "If screaming and shouting would get me the extra two points, I would do it, believe me. But we know that you can't do anything about that decision.
"The referee (Martin Atkinson) could see it live that Kyle Walker pulls Jean Beausejour's shoulder.
"If he (Atkinson) is looking at the ball, that is why he has missed it, but you can't understand why the linesman doesn't flag for it.
"We are too honest - maybe if he (Beausejour) had gone to ground, we would have had a free-kick."
But asked if he had had a word with Beausejour about being "too honest", Martinez said: "No - we are an honest team and I do believe that over the course of the season, if you are honest, the footballing gods will smile on you. So I hope that is the case."
Tottenham remain fifth with four matches to go, level on points with fourth-placed Chelsea and a point behind third-placed Arsenal.
Sunday's fixtures see Chelsea play Swansea at home and Arsenal host champions Manchester United.
And asked whether he regarded Saturday's result as two points dropped or a point gained in the pursuit of Champions League football, Spurs boss Andre Villas-Boas said: "It depends on the results tomorrow [Sunday] of our opponents. It is intimately related to that.
"We can still be in control of our own destiny or not after tomorrow's [Sunday] results.
"Normally away from home a point is important at this stage of the season.
"When everybody needs three points, I think it is a difficult situation for teams.
"It all depends on what happens tomorrow [Sunday]."
Meanwhile, Martinez is expecting Figueroa to be out for the rest of the season with a groin problem he sustained in the first half today while stretching in the box to make a good tackle on Spurs striker Jermain Defoe.
Soon after, he had to be carried from the field on a stretcher, and Martinez suggested in his post-match press conference that the Honduras international is now likely to miss the remainder of the campaign - which includes next month's FA Cup final against Manchester City.
Martinez said: ''The initial reaction is that Figueroa should be out for the season.
''It is a groin strain. It was (a great tackle), but the groin got stretched and the rest of the body pulled apart.
''We need to see the extent of the problem, but he is on crutches at the moment. We will assess him.''
Figueroa's injury comes a week after fellow defender Antolin Alcaraz picked up a hamstring problem that has brought the Paraguayan's own involvement in the cup final into doubt.